A fitness-based interferential genetics approach using hypertoxic/inactive gene alleles as references

Genetics, genomics, and biochemistry have all been of immense help in characterizing macromolecular cell entities and their interactions. Still, obtaining an overall picture of the functioning of even a simple unicellular species has remained a challenging task. One possible way to obtain a comprehensive picture has been described: by capitalizing on the observation that the overexpression on a multicopy plasmid of apparently any wild-type gene in yeast can lead to some negative effect on cell fitness (referring to the concept of “gene toxicity”), the FIG (fitness-based interferential genetics) approach was devised for selecting normal genes that are in antagonistic (and potentially also agonistic) relationship with a particular gene used as a reference. Herein, we take a complementary approach to FIG, by first selecting a “hypertoxic” allele of the reference gene—which easily provides the general possibility of obtaining gene products with the remarkable property of being inactive without altering their macromolecular interactivity—and then looking for the genes that interact functionally with this reference. Thus, FIG and the present approach (Trap-FIG), both taking advantage of the negative effects on cell fitness induced by various quantitative modulations in cellular networks, could potentially pave the way for the emergence of efficient in situ biochemistry.     

Problem-based learning in veterinary medicine: protein metabolism

A problem-based approach to teaching biochemistry to veterinary students is described which aims to encourage the finding and learning of biochemical information that is relevant to real-life veterinary problems.     

The role of fish studies in estuarine pollution assessment

The environmental quality objective and standards (EQO/EQS) approach to controlling and assessing estuarine pollution is described together with details of the information necessary to assess the health of the fish populations and determine whether the EQO/EQS are being met in an estuary. These concepts are illustrated by examples from the Forth estuary, Scotland, involving studies of the ecology, pathology, biochemistry and contaminant bioaccumulation of fish in relation to the benthos, water quality and anthropogenic influences.     

Sustaining the development and implementation of student-centered teaching nationally: the importance of a community of practice

Although the idea of using a workshop to educate potential users about a set of materials or techniques is not new, the workshops described here go beyond simple dissemination and create ongoing communities of practice that support widespread and sustained improvement in the biochemistry classroom. The degree to which pedagogical innovations improve student learning on a national level depends on how broadly they are disseminated and how they are implemented and sustained. Workshops can be effective in disseminating ideas and techniques, but they often fail to sustain implementation. This paper describes Core Collaborators Workshops (CCWs) that were specifically designed for biochemistry faculty to improve the quality of active learning materials, support faculty in transforming their classrooms, and disseminate these efforts nationally. This CCW model proved very effective to date as shown by the fact that, 8 months after the last CCW, all workshop participants reported using at least some of the instructional materials discussed during the workshop. In addition, participants remarked that the superior community building and direct mentoring available through the CCWs greatly increased their confidence in implementing this new curricular approach and has made them more likely to act as leaders themselves.     

本科生物技术综合性超大实验课程的架构与建设

为了培养本科生的分子生物学实验设计与操作技能,在实践教学中实现培养本科创新人才的目标,以用大肠杆菌发酵生产重组细菌碱性磷酸酶为案例,通过碱性磷酸酶基因的克隆、原核表达、发酵生产、提取纯化以及酶活性检测等系列实验,把本科的基因工程、发酵工程和生物化学3门综合性独立实验课程有机地组合成一个内容相关联的超大型综合性生物技术大实验,进一步凸显了生物技术中以基因工程技术为核心的上游核酸操作、中游发酵生产和下游蛋白分离纯化三大技术模块的有机联系,大大地提高了本科实验教学的综合性和研究性,提升了实践教学水平,取得了良好的教学效果。     

Attracting friends to feast on foes: engineering terpene emission to make crop plants more attractive to herbivore enemies

When attacked by herbivorous insects or mites, some plant species call on other arthropods for help. They emit mixtures of volatile compounds, dominated by terpenes, to attract carnivorous arthropods that prey on or parasitise herbivores and so reduce further damage. This fascinating defence strategy offers a new, environmentally friendly approach to crop protection. Using recent advances in the biochemistry and molecular genetics of terpene biosynthesis, it should now be possible to engineer crop plants that release terpenes for attracting herbivore enemies. By introducing or selectively altering the existing rate of terpene emission and composition, plant breeders could enable attacked plants to attract enemies and reduce additional herbivory, without compromising the effectiveness of other modes of defence.     

An improved culture system for virus isolation and detection

Cell culture plays an important role in virology. It provides a platform for the detection and isolation of viruses as well as for the biochemistry and molecular biology based studies of viruses. In the present work, a new system that could permits multiple (different) cell lines to be simultaneously cultured in one dish was developed. In the system, each cell line was cultured in an isolated zone in the same dish or well and the system is therefore called an isolated co-culture system. The usefulness of this novel approach for virus isolation was demonstrated using a model system based on adenovirus.     

High blood pressure: hunting the genes.

High blood pressure is a disease of unknown cause. Family history of the disease indicates higher risk, but it is not known which genes are involved or how they interact with environmental influences to produce the disorder. Molecular biology offers an approach to problems that have not so far been solved by classical physiology or biochemistry. By analysing polymorphic variation in chromosome markers such as minisatellite sequences, or by restriction fragment polymorphism analysis of candidate genes, attempts are being made to link genetic variations with hypertension. In genetically hypertensive rats, hypertension is associated with a polymorphism of the renin gene and with other loci on chromosomes 10 and 18. The role of these loci in human hypertension remains to be determined. Other genes such as sodium-lithium countertransport may be involved. Environmental factors such as stress or salt intake could influence the rate or timing of expression of certain genes and thus result in hypertension.     

Free energy simulations: Applications to the study of liquid water,hydrophobic interactions and solvent effects on conformational stability

Free energy simulations using the Metropolis Monte Carlo method and the coupling parameter approach with umbrella sampling are described for several problems of interest in structural biochemistry; the liquid water, the hydrophobic interaction of alkyl and phenyl groups in water and solvent effects on the conformational stability of the alanine dipeptide and the dimethyl phosphate anion in water. Proximity analysis of results is employed to identify stabilizing factors. Implications of result with respect to the structural chemistry of proteins and nucleic acids is considered.     

The digital language of amino acids

Summary. The subject of this paper is a digital approach to the investigation of the biochemical basis of genetic processes. The digital mechanism of nucleic acid and protein bio-syntheses, the evolution of biomacromolecules and, especially, the biochemical evolution of genetic language have been analyzed by the application of cybernetic methods, information theory and system theory, respectively. This paper reports the discovery of new methods for developing the new technologies in genetics. It is about the most advanced digital technology which is based on program, cybernetics and informational systems and laws. The results in the practical application of the new technology could be useful in bioinformatics, genetics, biochemistry, medicine and other natural sciences.     

Chemiluminescence quantitative immunohistochemical determination of MRP2 in liver biopsies.

Evaluation of protein expression in tissues and cells by electrophoretic and blotting techniques or by the quantification of the mRNA coding for the target protein is a common procedure in biochemistry research and clinical diagnoses. In this article, an alternative approach, based on an immunohistochemical procedure with chemiluminescent imaging detection, is described. The assay exploited the peculiar characteristics of the chemiluminescent detection of enzyme labels (high sensitivity and specificity, low background, easy quantification of the signal) for performing the direct, simple, and rapid quantitative evaluation of protein expression in tissues. When applied to the study of the levels of MRP2, a member of the human multidrug resistance-associated protein family, in samples obtained from formalin-fixed, paraffin-embedded liver biopsies, it allowed the reliable evaluation of the protein content of the tissue. Moreover, the analysis of clinical samples from patients with primary biliary cirrhosis under therapy with ursodeoxycholic acid gave results in line with those, previously reported in the literature, obtained with conventional protein expression analysis techniques.     

Microcomputers in biochemistry

The development of the microcomputer has meant that for the first time individual departments of biochemistry or even laboratories can have their own computing facilities. For less than the cost of a single-beam spectrophotometer it is possible to purchase a complete microcomputer system that is relatively easily programmed and operated. However, a considerable investment of labour is needed tom ake the microcomputer effective in biochemistry and it is a challenge to pare away the mystique from small-scale computing so that it becomes as common a tool as spectrophotometry. In the belief that there are few biochemists who could not benefit from the use of the microcomputer this brief article will explore some of the current and future applications of the microcomputer in biochemistry.     

Internal quality control samples for water bacteriology

A method is described for the preparation and application of a bacteriological quality control system for use with tests for plate counts and the enumeration of indicator organisms in water. Statistical limits are obtained and control charts prepared which are analagous to those used in analytical chemistry and clinical biochemistry laboratories. This approach has been applied successfully in this laboratory but needs to be tested more widely. Such numerically-based systems have seldom been attempted in microbiology, especially where multiple organisms have been included for the simultaneous control of several tests.     

II. Model Building: An Electrical Theory of Control of Growth and Development in Animals,Prompted by Studies of Exogenous Magnetic Field Effects (Paper I), and Evidence of DNA Current Conduction,In Vitro

A theory of control of cellular proliferation and differentiation in the early development of metazoan systems, postulating a system of electrical controls “parallel” to the processes of molecular biochemistry, is presented. It is argued that the processes of molecular biochemistry alone cannot explain how a developing organism defies a stochastic universe.

The demonstration of current flow (charge transfer) along the long axis of DNA through the base-pairs (the “π-way) in vitro raises the question of whether nature may employ such current flows for biological purposes. Such currents might be too small to be accessible to direct measurement in vivo but conduction has been measured in vitro, and the methods might well be extended to living systems. This has not been done because there is no reasonable model which could stimulate experimentation. We suggest several related, but detachable or independent, models for the biological utility of charge transfer, whose scope admittedly outruns current concepts of thinking about organization, growth, and development in eukaryotic, metazoan systems. The ideas are related to explanations proposed to explain the effects demonstrated on tumors and normal tissues described in Article I (this issue).

Microscopic and mesoscopic potential fields and currents are well known at sub-cellular, cellular, and organ systems levels. Not only are such phenomena associated with internal cellular membranes in bioenergetics and information flow, but remarkable long-range fields over tissue interfaces and organs appear to play a role in embryonic development (Nuccitelli, ). The origin of the fields remains unclear and is the subject of active investigation. We are proposing that similar processes could play a vital role at a “sub-microscopic level,” at the level of the chromosomes themselves, and could play a role in organizing and directing fundamental processes of growth and development, in parallel with the more discernible fields and currents described.     

Ommochromes in invertebrates: biochemistry and cell biology

Ommochromes are widely occurring coloured molecules of invertebrates, arising from tryptophan catabolism through the so‐called Tryptophan → Ommochrome pathway. They are mainly known to mediate compound eye vision, as well as reversible and irreversible colour patterning. Ommochromes might also be involved in cell homeostasis by detoxifying free tryptophan and buffering oxidative stress. These biological functions are directly linked to their unique chromophore, the phenoxazine/phenothiazine system. The most recent reviews on ommochrome biochemistry were published more than 30 years ago, since when new results on the enzymes of the ommochrome pathway, on ommochrome photochemistry as well as on their antiradical capacities have been obtained. Ommochromasomes are the organelles where ommochromes are synthesised and stored. Hence, they play an important role in mediating ommochrome functions. Ommochromasomes are part of the lysosome‐related organelles (LROs) family, which includes other pigmented organelles such as vertebrate melanosomes. Ommochromasomes are unique because they are the only LRO for which a recycling process during reversible colour change has been described. Herein, we provide an update on ommochrome biochemistry, photoreactivity and antiradical capacities to explain their diversity and behaviour both in vivo and in vitro. We also highlight new biochemical techniques, such as quantum chemistry, metabolomics and crystallography, which could lead to major advances in their chemical and functional characterisation. We then focus on ommochromasome structure and formation by drawing parallels with the well‐characterised melanosomes of vertebrates. The biochemical, genetic, cellular and microscopic tools that have been applied to melanosomes should provide important information on the ommochromasome life cycle. We propose LRO‐based models for ommochromasome biogenesis and recycling that could be tested in the future. Using the context of insect compound eyes, we finally emphasise the importance of an integrated approach in understanding the biological functions of ommochromes.     

Single-cell dissection and microdroplet chemistry

The unique roles of individual cells may be critical to the physiology of an organism. In such cases, micromethods are essential to elucidating the molecular biology, biochemistry and biophysics of the specialized cells or even subcellular compartments of the important cells. The great proliferation of micromethods testifies to their value and no single review can be comprehensive. This review therefore provides only a generalized overview of one approach, namely dissection that provides a pure sample for subsequent extraction and analysis by microdroplet chemistry. As a means of illustrating the utility of this approach, an application-study of the interaction of cytosolic malate concentration and guard-cell phosphoenolpyruvate carboxylase-is provided.     

V.N. Karazin Kharkov National University as the foundation of biochemistry in Ukraine

The paper deals with the data on foundation and development of physiological chemistry (biochemistry) as independent science and education subject in the V. N. Karazin Kharkov National University before and after the organization of the Department of Physiological Chemistry. Studying the chemistry of natural compounds, their qualitative and quantitative content and transformations in living organisms both by foreign and home researchers made the basis for the appearance of physiological chemistry as static biochemistry. The improvement of the investigation methods and further discoveries caused the appearing of new branches--dynamic and functional biochemistry. The attention is paid to the fact that biochemistry arised at the Kharkov University as the education subject (A. I. Khodnev) and then developed as independent science due to efforts of A. Ya. Danilevskiy as well as biochemical school created by him. The Kazan' and Kharkov periods of scientific activity of A.Ya. Danilevskiy are described. The leading role of A. Ya. Danilevskiy in development of the home school of biochemistry is considered. Important role of A. V. Palladin in the foundation of Kharkov biochemists' school and organization of the Scientific-research Institute of Biochemistry in Kharkov is considered as well. It is stated that the Institute of Biochemistry after its arrival to Kiev and joining the Academy of Sciences became the center of Ukrainian biochemistry. The role of A. V. Nagorny and I. N. Bulankin in further development of biochemistry and foundation of a new scientific branch--age-related physiology and biochemistry--at the Kharkov University after its re-organization is discussed.     

Azaperone and sudden death of drive net-captured southern chamois

The use of tranquilizers in the capture of southern chamois (Rupicapra pyrenaica) for scientific and/or management purposes (collection of samples, marking, translocations) was studied to improve animal welfare during capture operations. We used clinical findings and a statistical approach to analyze the causes of six incidences of mortality during captures using drive nets and tranquilizers in this species. Hematology and serum biochemistry, pathology, the use of tranquilizers and their dosages, the number of people involved in the capture of the chamois, and the location were all taken into account. The selection of candidate models to explain mortality was conducted using the theoretic information approach. Both observational findings and the models selected suggested that high doses of azaperone and to a lesser extent haloperidol had an effect on mortality rates. The higher mean serum lactate concentrations found in the chamois that died suggests that fatigue levels increased drug sensitivity and provoked the appearance of adverse effects, thereby increasing the probability of death. We conclude that butyrophenones—and especially azaperone—have a low safety margin in the southern chamois, contrary to what has been described for other species.