Introduction to the special issue on molecular imaging in radiation biology

Molecular imaging is an evolving science that is concerned with the development of novel imaging probes and biomarkers that can be used to non-invasively image molecular and cellular processes. This special issue approaches molecular imaging in the context of radiation research, focusing on biomarkers and imaging methods that provide measurable signals that can assist in the quantification of radiation-induced effects of living systems at the physical, chemical and biological levels. The potential to image molecular changes in response to a radiation insult opens new and exciting opportunities for a more profound understanding of radiation biology, with the possibility of translation of these techniques to radiotherapy practice. This special issue brings together 14 reviews dedicated to the use of molecular imaging in the field of radiation research. The initial three reviews are introductory overviews of the key molecular imaging modalities: magnetic resonance, nuclear and optical. This is followed by 11 reviews each focusing on a specialist area within the field of radiation research. These include: hypoxia and perfusion, tissue metabolism, normal tissue injury, cell death and viability, receptor targeting and nanotechnology, reporter genes, reactive oxygen species (ROS), and biological dosimetry. Over the preceding decade, molecular imaging brought significant new advances to our understanding of every area of radiation biology. This special issue shows us these advances and points to the vibrant future of our field armed with these new capabilities.     

Critical review of Identification Techniques for Armillaria spp. and Heterobasidion annosum Root and Butt Rot Diseases

The need for a rapid and definite diagnosis of the Armillaria spp. and Heterohasidion annosum root and butt rot diseases as well as general requirements expected of a test to detect the pathogens are reviewed. As a spin-off from more fundamental molecular biological research there has been a remarkable increase in new methods for diagnosis (i.e. detection and identification) in recent years. These new methods all have in comtnon that they use strtjctural elements of the target organisms such as proteins, polysaccharides, glycoproteins, nucleic acids, etc. for the construction of antibodies, probes and primers for detection, or to produce electrophoretic patterns to be used for classification and identification. This paper presents a short review of principles, advantages, disadvantages and some perspectives of the new methods developed for Armillaria spp. and H. annosum diagnosis compared with conventional ones, such as interfertility testing or visual inspection of the pathogens in situ and in vitro in pure culture. It will be noted that the specificity and reproducibility of the new techniques, which are closely linked with potential experimental error, lead to principal pitfalls which should be kept in mind when conclusions are drawn on data generated by them.
Even though PCR-based methods become increasingly more widespread it is likely that most diagnostic methods will continue to be used or co-exist in some form in the future.     

Progress in research on radiation combined injury in China

The significant feature of radiation combined injury is the occurrence of a combined effect. For decades our institute has focused on studying the key complications of radiation-burn injury, including shock, suppression of hematopoiesis and immunity, gastrointestinal damage and local refractory wound healing. Here we summarize recent advancements in elucidating the mechanisms of and potential treatments for radiation combined injury. Concerning the suppression and regeneration of hematopoiesis in radiation combined injury, mechanisms of megakaryocyte damage have been elucidated and a new type of fusion protein stimulating thrombopoiesis has been developed and is being tested in animals. With regard to the damage and repair of intestinal epithelium, the important molecular mechanisms of radiation combined injury have been clarified, and new measures to prevent and treat gastrointestinal tract injury are proposed. With respect to the difficulties encountered in wound healing, the underlying causes of radiation combined injury have been proposed, and some potential methods to accelerate wound closure are under study. Systemic experiments have been done to determine the appropriate time for eschar excision and skin grafting, and the results provided significant insight into clinical treatment of the injury. In the search for early therapeutic regimens for severe burns and radiation combined injury to prevent deterioration of injuries and to improve survival, cervical sympathetic ganglion block was used for the treatment of animals with radiation combined injury and had significant benefits. These research advancements have potential for application in on-site emergency rescue and in-hospital treatment of radiation combined injury.     

Dynamically repairing and replacing neural networks: using hybrid computational and biological tools

The debilitating effects of injury to the nervous system can have a profound effect on daily life activities of the injured person. In this article, we present a project overview in which we are utilizing computational and biological principles, along with simulation and experimentation, to create a realistic computational model of natural and injured sensorimotor control systems. Through the development of hybrid in silico/biological coadaptive symbiotic systems, the goal is to create new technologies that yield transformative neuroprosthetic rehabilitative solutions and a new test bed for the development of integrative medical devices for the repair and enhancement of biological systems.     

Comparison of the diagnostic methods used in maxillofacial trauma

A prospective study was performed to evaluate the diagnostic methods used in acute maxillofacial trauma. Clinical examination, routine facial x-rays with linear tomography, and computer tomography were compared in 49 patients. Computer tomography was found to be the most accurate test in the diagnosis of facial bone injury, especially complex fractures. Computer tomography also provided valuable information regarding soft-tissue injury of the face. The radiation doses of linear tomography and computer tomography were calculated to be below the level known to cause cataract formation. Computer tomography is a safe, reliable adjunct in the diagnosis of acute maxillofacial trauma and should be strongly considered after initial screening measures are completed.     

Initial evaluation and follow-up of acute radiation syndrome in two patients from the Dakar accident

The aim of this work was to evaluate and follow up the evolution of radiation damage in two victims of a radiation accident. Blood samples were used for cytogenetic evaluation of radiation dose and heterogeneity. The radiation dose estimates were 1 Gy and 2.3 Gy in the two most exposed patients. Plasma was used for the measurement of the Flt3 ligand as a marker of haematopoietic aplasia, citrulline for damage to the jejunal mucosal epithelium and oxysterols for damage to the liver, the central nervous system and the vascular compartment. The use of these biological indicators demonstrated the presence of a haematopoietic syndrome and suggested the presence of subclinical radiation-induced damage to the liver in one of the two patients. These results support the interest in using these biological indicators in order to evaluate radiation damage, especially in complex accidental situations.     

Immunological approach in the diagnosis, therapy and prognosis of the exocrine pancreatic cancer

The aim of the paper is to outline the most important up-to-date methods regarding the immunological approach in the diagnosis, treatment and prognosis of the exocrine pancreatic cancer, keeping in mind that this localisation of neoplastic disease represents the 5th cause of cancer-related death and especially, an important cause of morbidity. This disease, diagnosed in the past in later stages, being therefore associated with poor results, has turned to be characterized by increasing survival rates due to the improvements in diagnostic and therapeutic methods. Regarding the diagnosis strategy, progress was made in imagistic sphera, aiming: 1. an early diagnosis of pancreatic cancer and, implicitly, a high resectability rate of tumor, and 2. an evaluation of the timing for palliative therapeutic methods. So that, if in the past the diagnostic algorithm meant endoscopic retrograde-cholangio-pancreatography, computed tomography and angiography, at present it means nuclear magnetic resonance and helicoidal tomography. Concerning the treatment, it has to be multidisciplinary (surgery, radiotherapy, chemotherapy, immunotherapy), complex, because, after a resection for cure (R0), the main stay of the treatment, the mean survival at 5 years is 3%-28% and the rate of recurrences is 33%-80%. Biological therapy (sometimes called immunotherapy, biotherapy or biological response modifier therapy) is a relatively new addition to the family of cancer treatments that also includes surgery, chemotherapy and radiation therapy. Biological therapies are designed to repair, stimulate or enhance the immune system responses. We shall try to point out how the exocrine pancreatic cancers, the same stages and undergoing the same approaches, have had different responses due to a different biological behavior and how the biological response modifiers (interferons, interleukins, colony-stimulating factors, monoclonal antibodies and vaccines) can improve the results in pancreatic cancer.     

Molecular epidemiology of the late radiation effects

The scientific bases, problems, methods and prospects for the development of a new scientific direction "Molecular epidemiology of late consequences of ionizing radiation influence on the man" are reviewed. It is marked, that for two decades on the basis of achievements in the field of molecular biology, biochemistry, genetics and genomics it has arisen and is developing the important direction in infectious and non-infectious epidemiology--molecular epidemiology. Molecular epidemiology is a new section of epidemiology on border with molecular biology and genetics, integrating efforts of epidemiologists, molecular biologists, genetics and researchers from many other areas of knowledge in a direction of an estimation of individual risk of development of chronic diseases at practically healthy people, development of recommendations on their preventive maintenance in cohorts of risk and, hence, in all population by studying by molecular methods of an etiology of illnesses, mechanisms of a susceptibility to them, and also biological mechanisms and frequency of their development in human cohorts. Special development in molecular epidemiology was noticed for the methods named biomarkers, subdivided on 4 categories: 1) markers of an internal dose; 2) markers of an effective dose; 3) markers of preclinical biological effects; 4) markers of a susceptibility. Use of biomarkers in molecular-epidemiological researches appeared especially productive in oncology. As radiogenic cancers are the main remote consequence of exposure to ionizing radiations, approaches and achievements of molecular epidemiology of nonradiation cancers are perspective at becoming of molecular epidemiology of radiation effects, with an object to solve problems concerning mechanisms and features of radiation carcinogenesis, risk assessment, distribution and preventive maintenance of radiogenic cancers in cohorts of professionals of the various branches having contact to sources of ionizing radiation, and the population, exposed to radiation medically.     

Wnt signalling pathway in bladder cancer

Bladder cancer (BC) is one of the most common tumours of the urinary system and is also known as a highly malignant tumour. In addition to conventional diagnosis and treatment methods, recent research has focused on studying the molecular mechanisms related to BC, in the hope that new, less toxic and effective targeted anticancer drugs and new diagnostic markers can be discovered. It is known that the Wingless (Wnt) signalling pathway and its related genes, proteins and other substances are involved in multiple biological processes of various tumours. Clarifying the contribution of the Wnt signalling pathway in bladder tumours will help establish early diagnosis indicators, develop new therapeutic drugs and evaluate the prognosis for BC. This review aims to summarise previous studies related to BC and the Wnt signalling pathway, with a focus on exploring the participating substances and their mechanisms in the regulation of the Wnt signalling pathway to better determine how to promote new chemotherapeutic drugs, potential therapeutic targets and diagnostic biomarkers.     

Epithelial carcinogenesis in the mouse: correlating the genetics and the biology.

Tumour formation relies on a complex combination of genetic and environmental factors. In particular, the contributions from inherited predisposition genes as well as carcinogens, for example from cigarettes or in the diet, are amongst the major contributors to tumorigenesis. Since the study of such processes in particularly difficult in human cancers, the availability of a well-defined model system is of obvious benefit. The mouse skin model of multistage carcinogenesis offers an excellent tool for the study of the target cells, the target genes and the biological events associated with neoplasia. In this system, tumorigenesis occurs in a series of defined stages, each of which is characterized by specific and reproducible alterations in genes such as H-ras, cyclin D1, p53 and p16INK4A. Additional changes occur in the production of, or response to, factors such as transforming growth factor beta (TGF beta). These genetic and biological alterations are mirrored in human tumours of epithelial origin. Hence, research into the general principles of tumour initiation, promotion and progression in the context of the mouse skin model is likely to prove valuable in the continual search for new methods for the diagnosis, prevention, and therapeutic treatment of human cancers.     

The decomposition of the EPR spectra of multicomponent systems irradiated at 77 K into paramagnetic center signals of different natures]

Main principles of the way to decompose an EPR spectrum of a multicomponent system, irradiated at 77 K, into separate radiation-induced paramagnetic centre signals are given. The decomposition is possible due to the computer assistant spectra processing, and is based on different properties of different paramagnetic centres, namely, on different thermostability of the centres, on different rate of relaxation, and on different photosensitivity. Concrete examples of the EPR spectrum decomposition into different free radical signals are given for cases of murine liver and spleen irradiated at 77 K. Radiochemical yields of different free radicals, induced by gamma radiation at 77 K in whole biological tissues, were defined. The data on nature and properties of the paramagnetic centres induced by radiation in biological tissues are shortly reviewed.     

新型脱氮微生物与水体脱氮新工艺研究进展

氨氮是河流等淡水资源有机污染的主要污染指标之一。生物脱氮具有低成本、高效、无二次污染和易操作等优点,极具发展前景。重点概述了水体净化系统中新型脱氮微生物的种类及研究进展,介绍了厌氧氨氧化、短程硝化-反硝化和分段进水生物脱氮等高效节能新工艺的工艺原理。     

Modern problems of biodosimetry

Humans have different radiosensitivity. Besides, many factors which are not under control can change significantly biological effects of radiation. Some of substances are present in our food--residual amounts of fertilizers or herbicides can be mutagenic or influence mutagenic action of radiation. In the last case synergetic or antagonistic effects can be observed. At the same time many food products contain radioprotectors or antimutagens. Some drugs, stress, virus diseases and so on can change biological effects of radiation too. Radioadaptive response is one of the most significant factors which can be responsible for incorrect radiation dose evaluation. All these uncontrolled factors may be responsible for significant mistakes of evaluating radiation dose by biological methods. That is why biological methods can be used for bioindication but not for biodosimetry.     

A New Distribution-Free Approach to Constructing the Confidence Region for Multiple Parameters

Construction of confidence intervals or regions is an important part of statistical inference. The usual approach to constructing a confidence interval for a single parameter or confidence region for two or more parameters requires that the distribution of estimated parameters is known or can be assumed. In reality, the sampling distributions of parameters of biological importance are often unknown or difficult to be characterized. Distribution-free nonparametric resampling methods such as bootstrapping and permutation have been widely used to construct the confidence interval for a single parameter. There are also several parametric (ellipse) and nonparametric (convex hull peeling, bagplot and HPDregionplot) methods available for constructing confidence regions for two or more parameters. However, these methods have some key deficiencies including biased estimation of the true coverage rate, failure to account for the shape of the distribution inherent in the data and difficulty to implement. The purpose of this paper is to develop a new distribution-free method for constructing the confidence region that is based only on a few basic geometrical principles and accounts for the actual shape of the distribution inherent in the real data. The new method is implemented in an R package, distfree.cr/R. The statistical properties of the new method are evaluated and compared with those of the other methods through Monte Carlo simulation. Our new method outperforms the other methods regardless of whether the samples are taken from normal or non-normal bivariate distributions. In addition, the superiority of our method is consistent across different sample sizes and different levels of correlation between the two variables. We also analyze three biological data sets to illustrate the use of our new method for genomics and other biological researches.     

基于智能计算噬菌体的细菌宿主范围预测

针对噬菌体的细菌宿主范围预测对于深入理解噬菌体及将其作为抗生素替代用于生物疗法具有重要意义。传统生物实验方法确定噬菌体的细菌宿主范围受到极有限的噬菌体可培养性和严苛的培养条件限制,而高通量测序技术所提供的海量基因组或宏基因组序列提供了噬菌体及细菌重要的序列信息,因此智能计算为预测噬菌体的细菌宿主范围提供了可行方法。本文从智能计算的角度对噬菌体的细菌宿主范围预测研究进行系统梳理,从噬菌体感染细菌的过程入手,描述配对预测模型所依赖的特征及其生物合理性,归纳宿主范围预测的智能模型、建模原理及预测策略,总结建模训练和评估所依赖的参考数据集与真实数据及评价指标。本文特别注意挖掘和分析各信息手段、模型、方法其背后的生物合理性及其依赖的生物机理。本综述期望推动基于智能算法的噬菌体的细菌宿主范围预测研究发展,并探索将生物先验结合人工智能实现噬菌体侵袭细菌宿主的本质机理推断,同时也为基于噬菌体的临床应用提供参考与借鉴。     

Do we still need supertrees?

The up-dated species level phylogeny for the carnivores using a supertree approach provides new insights into the evolutionary origin and relationships of carnivores. While the gain in biological knowledge is substantial, the supertree approach is not undisputed. I discuss the principles of supertree methods and the competitor supermatrix approaches. I argue that both methods are important to infer phylogenetic relationships.     

Co-construction of an assessment method of the environmental sustainability for cattle farms involved in a Protected Designation of Origin (PDO) cheese value chain,Cantal PDO

In France, numerous Protected Designation of Origin (PDO) cheese value chains have revised their specifications to address environmental protection, particularly at the farm level. In this stage, it is nevertheless impossible to state whether the proposed modifications may ensure the sustainability of environmental protection as no environmental sustainability diagnostic has been conducted. The aim of this study is to construct an assessment method for the Cantal PDO farms.A multi-criteria assessment approach was implemented in the following 5 steps: definition of the framework of the study, determination of the principles and criteria, definition of the indicators, aggregation of all elements of the assessment, and finally, test of the assessment method on farms. Focus groups meetings were organised for the first four steps. The panel discussions were based on data obtained from both the literature and surveys of stakeholders operating in the value chain and within the territory.The obtained assessment method comprises 4 principles characterised by 33 indicators. The most important principle (45%), management of grassland resources, is a key economic and environmental point of the studied farms. It reflects the necessary intensive use of grass by the animals in the PDO farms. Few existing methods addressed this principle that required the design of several new indicators. The second principle, impact of agricultural practices (25%), is often included in environmental sustainability assessment methods The adopted indicators are, thus, drawn from existing methods and adapted to the context of the farms studied. The management of the farm buildings and the landscape principle (18%) is often considered in social sustainability. Its role in environmental sustainability can be explained by its strong link with the image of PDO products. Primarily drawn from the literature, the used indicators have been extended to make the assessment method as objective as possible. Finally, the management of local, energy and water resources principle has the lowest weighting (12%). This can be explained by the limited number of indicators.This assessment method was constructed for the Cantal PDO farms by considering their environment and particularities. In consequence, the stakeholders have taken ownership of it. It could be used by other ruminant systems based on grassland. The development of numerous indicators enhanced the pool of existing indicators. This assessment method was sensitive and allowed for the discrimination between farms.     

Genomic instability, bystander effects and radiation risks: implications for development of protection strategies for man and the environment

The last few years has seen what people are now referring to as a "shifting Paradigm" in our way of thinking about radiation effects on biological systems. The concept of the central role of DNA damage due to double strand breaks induced by a radiation "hit" has been itself hit by many studies showing persistent effects in the distant progeny of radiation exposed cells. This phenomenon is known as radiation induced genomic instability. More recently evidence has been accumulating that not even the parent cell need be exposed to radiation (the bystander effect). The new paradigm suggests that cellular stress responses or damage signalling through a range of signal transduction pathways are involved and that cell-cell contact or secretion of damage signalling molecules can induce responses in undamaged and unirradiated cells. Are these new effects relevant to risk assessment, or does it matter HOW radiation affects cells if we have good epidemiological evidence of which to base our risk estimates? The aim of this paper is to introduce the new concepts and to consider reasons why they might alter our methods of risk estimation. The paper also considers the impact of the new concepts on environmental protection and discusses the need for research in the field of comparative radiobiology if we are to develop policies which can adequately protect biodiversity.     

The ecology of visual landscapes: Exploring the conceptual common ground of visual and ecological landscape indicators

This paper explores the conceptual common ground between visual and ecological landscape indicators. Indicators can be used to summarise complex information about landscape functions and the ability to extract a common set of indicators for analysing different landscape functions may provide valuable support for multiple-use planning.The development of landscape ecological indicators has been a very active research field that has resulted in a wide range of landscape metrics and composite indices with a strong conceptual base in landscape ecological principles. For the visual aspects of landscapes, however, this conceptual base is often missing and thus hindering progress in the development of indicators. This paper presents the results of an analysis of the correspondence between ecological indicators and visual indicators in order to explore whether there is common ground in both concept and operation. The conceptual level is presented for both ecological and visual indicators, as it is the concepts that define their aim and scope. We feel that transparency over this issue is crucial to the development and use of environmental indicators. The approach identified a candidate set of indicators that capture important aspects of both ecological and visual quality. The strength of the approach is that it forces us to focus on the identification of what we wish to indicate by means of landscape theory and assessment that are relevant to a specific landscape context. We believe that the approach presented here forms the basis for development of new methods for understanding the impact of landscape change in a management and planning context.