The types of homology and their significance for evolutionary biology and phylogenetics

This paper comments on recently revived discussion about the most adequate definition of homology. Homologues are considered as similarities of complex structures or patterns which are based on a continuity of biological information or instruction. Dependent on the level of comparison four types of homology are defined: (1) Iterative ( = serial = homonomy), (2) ontogenetic, (3) di- or polymorphic, and (4) supraspecific homology. The significance of all four types for evolutionary biology and phylogenetic analysis is outlined.     

The weapon potential of a microbe

The designation of a microbe as a potential biological weapon poses the vexing question of how such a decision is made given the many pathogenic microbes that cause disease. Analysis of the properties of microbes that are currently considered biological weapons against humans revealed no obvious relationship to virulence, except that all are pathogenic for humans. Notably, the weapon potential of a microbe rather than its pathogenic properties or virulence appeared to be the major consideration when categorizing certain agents as biological weapons. In an effort to standardize the assessment of the risk that is posed by microbes as biological warfare agents using the basic principles of microbial communicability (defined here as a parameter of transmission) and virulence, a simple formula is proposed for estimating the weapon potential of a microbe.     

Practical application of synthetic biology principles

Synthetic biology can be defined as the “repurposing and redesign of biological systems for novel purposes or applications, ” and the field lies at the interface of several biological research areas. This broad definition can be taken to include a variety of investigative endeavors, and successful design of new biological paradigms requires integration of many scientific disciplines including (but not limited to) protein engineering, metabolic engineering, genomics, structural biology, chemical biology, systems biology, and bioinformatics. This review focuses on recent applications of synthetic biology principles in three areas: (i) the construction of artificial biomolecules and biomaterials; (ii) the synthesis of both fine and bulk chemicals (including biofuels); and (iii) the construction of “smart” biological systems that respond to the surrounding environment.     

Governance of genetic biocontrol technologies for invasive fish

The modification of living agents for biological control can be collectively regarded as genetic biocontrol (GBC). Applications to invasive fish are an area of significant work in GBC, employing a diversity of techniques. Some of these techniques are governed by particular legislation, policy or treaty, (e.g., transgenesis), while others deliver agents with similar properties with minimal regulation. Together, this heterogeneity of governance and biology creates a number of challenges for effective use of GBC. In some cases, there are gaps and inconsistencies that pose real threats to biodiversity, and the long term sustainability of oversight arrangements as they currently stand is questionable. Researchers and would-be users of GBC for invasive fish must proactively engage with a variety of stakeholders to improve governance (in fish and other taxa), which we contend may include reconfiguration of relevant national governance systems, meaningful stakeholder dialogue and the creation of a new international treaty dedicated to biological control.     

The dual-use dilemma for the life sciences: perspectives, conundrums, and global solutions

The term "dual-use" traditionally has been used to describe technologies that could have both civilian and military usage, but this term has at least three different dimensions that pose a dilemma for modern biology and its possible misuse for hostile purposes: (1) ostensibly civilian facilities that are in fact intended for military or terrorist bioweapons development and production; (2) equipment and agents that could be misappropriated and misused for biological weapons development and production; and (3) the generation and dissemination of scientific knowledge that could be misapplied for biological weapons development and production. These three different aspects of the "dual-use dilemma" are frequently confused--each demands a distinct approach within a "web of prevention" in order to reduce the future risk of bioterrorism and biowarfare. This article discusses the nature of the different perspectives and divergent approaches as a contribution to finding a scientifically acceptable global solution to the problem posed by the dual-use dilemma. We propose that: (1) facilities that are intended for bioweapons development and production should be primarily prevented by a strengthened Biological and Toxin Weapons Convention (BTWC) effectively implemented in all nation states, one that includes provisions for adequate transparency to improve confidence and a mechanism for thorough inspections when there is sufficient cause, and enhanced law enforcement activities involving international cooperation and sharing of critical intelligence information; (2) potentially dual-use equipment and agents should be available to legitimate users for peaceful purposes, but strengthened national biosafety and physical and personnel biosecurity controls in all nations together with effective export controls should be implemented to limit the potential for the misappropriation of such equipment and materials; and (3) information should be openly accessible by the global scientific community, but a culture of responsible conduct involving the breadth of the international life sciences communities should be adopted to protect the ongoing revolution in the life sciences from being hijacked for hostile misuse of the knowledge generated and communicated by life scientists.     

Biologie et politique IV. — Questions d'éthique

Within the framework of the increasing development of techniques and technology, Humankind is often considered and used as an instrument. Because power from the industry can generate bad consequences that are unforeseeable and thus out of a comprehensive control, new thoughts on Mankind and its values are needed. The moral code gives the practical distinction between good and evil. Ethics calls to a reflection from free, reasonable and responsible beings. Numerous groups of thoughts working for a progressive emergence of universally admitted ethic rules that should allow the offer of an international right of ‘Human rights’ are now available at different levels, i.e. professional, national, international. From the biomedical ethic, it appears that Human beings, considered as biological entities, have the right to live, that the embryo must not be used as an usual research material and that the diagnostic of embryos before implantation must be exceptional. Human being has a right to dignity. This means that one must not be submitted to degrading treatments (torture, slavery, …), must have access to health care, must not constitute an experimental object, the germinal cells must not be manipulated and neither his body or its constituting elements must ever be commercialised or patented. Corpses need respect and any attack to their integrity (in order to extract profits for public health, science, justice…) must be justified. A person, defined here as a self-awa-reness constructed in function of other persons, must be free (i.e. his consent is absolutely needed for a diagnostic or experimental treatment) and has economical, social and cultural rights. French laws do not permit a person to choose his death The international law progressively refines a definition of crime against humanity (ethnic extinction, torture, rape…). In the ethics for environment, the respect of men towards animals considered as individuals and species in the framework of the conservation of the nature and genetics resources, is taken into account rather than the rights of animals per se. Finally, an arsenal of agreements, directives and legislation at local, national and international levels attempts to harmonise the practices of the technoscience with the concept of long lasting development, in order to maintain the higher-order balances within ecosystems. Mankind felt itself responsible of the environment for the future generations. Nevertheless, any regulation in the matter of ethic remains a compromise within contradictory views. The only general rule for every one, remains not to harm others, and to give oneself to others. This is, for long time, the traditional basis of religious preachments, although its success remains relatively controversial.     

鼠疫减毒活疫苗研究现状与展望

鼠疫(plague)是由鼠疫耶尔森氏菌(Yersinia pesits)引起的烈性传染病,在人类历史上曾造成约2亿人的死亡,在我国被列为甲类传染病。由于鼠疫菌具有高度致病性、传染性,被列为最具潜力的生物战剂和生物恐怖剂。在面临鼠疫威胁时,疫苗是最为有力的武器。鼠疫疫苗研究中,减毒活疫苗是重要的研究方向,现就鼠疫减毒活疫苗的研究现状进行综述,为新疫苗的研制提供参考。     

<Emphasis Type="Italic">Bacillus anthracis</Emphasis>, <Emphasis Type="Italic">Francisella tularensis</Emphasis> and <Emphasis Type="Italic">Yersinia pestis</Emphasis>. The most important bacterial warfare agents — <Emphasis Type="Italic">review</Emphasis>

There are three most important bacterial causative agents of serious infections that could be misused for warfare purposes: Bacillus anthracis (the causative agent of anthrax) is the most frequently mentioned one; however, Fracisella tularensis (causing tularemia) and Yersinia pestis (the causative agent of plague) are further bacterial agents enlisted by Centers for Disease Control and Prevention into the category A of potential biological weapons. This review intends to summarize basic information about these bacterial agents. Military aspects of their pathogenesis and the detection techniques suitable for field use are discussed.     

Implementation of biosurety systems in a Department of Defense medical research laboratory

New biosurety regulations and guidelines were implemented in 2003 because of increased concern for the safety and security of biological select agents and toxins (BSAT) that may be used as weapons of mass destruction. Biosurety is defined as the combination of security, biosafety, agent accountability, and personnel reliability needed to prevent unauthorized access to select agents of bioterrorism. These new regulations will lead to increased scrutiny of the use of select biological agents in registered research laboratories, but the regulations may have unintended effects on cost, progress, and perceptions in programs previously considered part of the academic research community. We review the history of biosurety, evolving guidelines, implementation of the regulations, and impacts at the lead research laboratory for medical biological defense for the Department of Defense.     

Antibodies for biodefense

Potential bioweapons are biological agents (bacteria, viruses, and toxins) at risk of intentional dissemination. Biodefense, defined as development of therapeutics and vaccines against these agents, has seen an increase, particularly in the US following the 2001 anthrax attack. This review focuses on recombinant antibodies and polyclonal antibodies for biodefense that have been accepted for clinical use. These antibodies aim to protect against primary potential bioweapons, or category A agents as defined by the Centers for Disease Control and Prevention (Bacillus anthracis, Yersinia pestis, Francisella tularensis, botulinum neurotoxins, smallpox virus, and certain others causing viral hemorrhagic fevers) and certain category B agents. Potential for prophylactic use is presented, as well as frequent use of oligoclonal antibodies or synergistic effect with other molecules. Capacities and limitations of antibodies for use in biodefense are discussed, and are generally applicable to the field of infectious diseases.     

Bioterrorism: responding to an emerging threat

Only a few years ago bioterrorism was considered a remote concern but few today are complacent about the possibility of biological agents being intentionally used to cause widespread panic, disruption, disease and death. By its very nature, the biological weapons threat - with its close links to naturally occurring infectious agents and disease - requires a different paradigm than that for conventional terrorism, military strikes or attacks caused by other weapons of mass destruction. This evolving threat presents the medical, public health and scientific communities (importantly including biotechnology) with a set of difficult and pressing challenges. This article provides a brief overview of the threat from biological weapons, the nature of a bioterrorist attack and some of the issues that need to be addressed if we are to make meaningful progress to prevent or contain this disturbing and potentially catastrophic danger.     

Hazards,threats and risks: lessons from the past to a defensive attitude for the future

Since ever infectious diseases have been a major hazard for the armed forces in operations. Nowadays our nations are facing the threat of terrorism, including bioterrorism. This threat is much more related to the potential disorganization of the society than to the lethal effects of the agents. Biological weapons are considered more like terror weapons than like mass destruction weapons, hence the importance of preparing specific defence measures. The know-how acquired from the struggle against natural infectious diseases is a useful help to face the biological weapon threats and risks. Likewise, the defence attitude is based on three pillars: anticipating, managing, and restoring. This military as well as civilian defence attitude applies to six important functions: (1) alert, (2) detection, diagnosis and identification, (3) medical countermeasures (drugs, vaccines and sera), (4) medical care in hospital, (5) training and information, (6) research and development of dedicated technologies.     

Antibodies for biodefense

Potential bioweapons are biological agents (bacteria, viruses and toxins) at risk of intentional dissemination. Biodefense, defined as development of therapeutics and vaccines against these agents, has seen an increase, particularly in the US, following the 2001 anthrax attack. This review focuses on recombinant antibodies and polyclonal antibodies for biodefense that have been accepted for clinical use. These antibodies aim to protect against primary potential bioweapons or category A agents as defined by the Centers for Disease Control and Prevention (Bacillus anthracis, Yersinia pestis, Francisella tularensis, botulinum neurotoxins, smallpox virus and certain others causing viral hemorrhagic fevers) and certain category B agents. Potential for prophylactic use is presented, as well as frequent use of oligoclonal antibodies or synergistic effect with other molecules. Capacities and limitations of antibodies for use in biodefense are discussed, and are generally applicable to the field of infectious diseases.Key words: antibody, anthrax, plague, smallpox, botulism, tularemia, brucellosis, hemorrhagic, ricin, SEB     

保护生物学概要

保护生物学的形成是对生物危机的反应和生物科学迅速发展的结果。它是应用科学解决由于人类活动干扰或其它因素引起的物种、群落和生态系统出现的问题的新学科。其”目的是提供保护生物多样性的原理和工具“,其基础科学和应用科学的综合性交叉学科。系统学、生态学、生物地理学和种群生态学的原理和方法是保护生物学重要的理论和实践基础。     

Mystery of mysteries: Darwin and the species problem

Darwin offered an intriguing answer to the species problem. He doubted the existence of the species category as a real category in nature, but he did not doubt the existence of those taxa called “species”. And despite his scepticism of the species category, Darwin continued using the word “species”. Many have said that Darwin did not understand the nature of species. Yet his answer to the species problem is both theoretically sound and practical. On the theoretical side, Darwin’s answer is confirmed by contemporary biology, and it offers a more satisfactory answer to the species problem than recent attempts to save the species category. On the practical side, Darwin’s answer frees us from the search for the correct theoretical definition of “species”. But at the same time it does not require that we banish the word “species” from biology as some recent sceptics of the species category advocate. © The Willi Hennig Society 2010.     

Category of exposure to HIV and age in the progression to AIDS: longitudinal study of 1199 people with known dates of seroconversion. HIV Italian Seroconversion Study Group.

OBJECTIVES: To determine whether rate of development of AIDS is affected by category of exposure to HIV and whether the more rapid development found in older subjects persists for each exposure category. DESIGN: Longitudinal study of people with known date of seroconversion to HIV. SETTING: 16 HIV treatment centres throughout Italy. SUBJECTS: 1199 people infected with HIV through use of injected drugs, homosexual sex, or heterosexual sex. MAIN OUTCOME MEASURES: AIDS as defined by 1987 definition of Centers for Disease Control (including and excluding neoplasms) and by 1993 European definition. RESULTS: 225 subjects (18.8%) progressed to AIDS (Centers for Disease Control 1987 definition) during median follow up of 5.8 years. Univariate analyses showed more rapid progression to AIDS for older subjects compared with younger subjects and for homosexual men compared with other exposure categories. The age effect was of similar size in each exposure category and in men and women. In a bivariate model with age and exposure categories simultaneously included as covariates, differences by exposure category disappeared for use of injected drugs and heterosexual sex compared with homosexual sex (relative hazards 1.02 (95% confidence interval 0.71 to 1.45) and 1.07 (0.70 to 1.64) respectively), while the age effect remained (relative hazard 1.55 (1.32 to 1.83) for 10 year increase in age). Analyses using the other definitions for AIDS did not appreciably change these results. CONCLUSIONS: There was no evidence of differences in rate of development of AIDS by exposure category, while there was a strong tendency for more rapid development in older subjects for all three groups. This supports the view that external cofactors do not play major role in AIDS pathogenesis but that age is of fundamental importance.     

Is there a special conservation biology?

Conservation biology is special to the extent that it fills useful roles in the scientific and conservation fields that are not being filled by practitioners of other disciplines. The emergence of the “new conservation biology” in the late 1970's and its blossoming in the 1980's and 1990's reflect, to a large degree, a failure of traditional academic ecology and the natural resource disciplines to address modern conservation problems adequately. Yet, to be successful conservation biology, as an interdisciplinary field, must build on the strengths of other disciplines both basic and applied. The new conservation biology grew out of concern over extinction of species, although the field has expanded to include issues about management of several levels of biological organization. I examine four controversial questions of importance to conservation biologists today: 1) are there any robust principles of conservation biology? 2) Is advocacy an appropriate activity of conservation biologists? 3) Are we educating conservation biologists properly? 4) Is conservation biology distinct from other biological and resource management disciplines? I answer three of these questions with a tentative “yes” and one (3) with a regretful “in most cases, no.” I see a need for broader Training for students of conservation biology, more emphasis on collecting basic field data, compelling applications of conservation biology to real problems, increased influence on policy, and expansion of the international scope of the discipline. If all these occur, conservation biology will by truly special.     

Where is biological therapy going?

The substantial progress in our understanding of molecular and cellular biology has allowed us to design biological therapeutics ('biologicals') with defined targets and effector functions. These biologicals have greatly contributed to our current knowledge of pathogenetic mechanisms in autoimmune diseases. However, although some of the biologicals have been extremely successful in treating the symptoms of chronic inflammation, biological therapy has not yet met the expectations of permanently silencing the chronic immune response. In this commentary we discuss current concepts and future directions of biological therapy, and the potential usefulness of biologicals as a treatment of human autoimmune diseases in appropriate critical applications with the use of suitably designed agents.     

Are island‐like systems biologically similar to islands? A review of the evidence

Islands are geographically defined as land masses completely surrounded by water, and island systems have been used as models for many biogeographic, ecological, and evolutionary theories ever since Darwin's pioneering efforts. However, their biological definition is complex. Over the past few decades these theories have been applied to many study systems that only share some geographic features with island systems. These features include spatial fragmentation, limited area, spatial and temporal isolation from adjacent parts of the system, and low connectivity between different parts within the system, to mention just a few. These systems vary in their form, the matrix that surrounds them, the factors defining their borders, the extent of insularity they impose on the different taxa, and their geological similarity to different types of actual islands. Here, I seek to understand whether such island‐like systems (ILS) function biologically as true islands. In the first part, I describe the wide diversity of ILS suggested in the literature and the variation in the features that define their insularity. In the second part, I review the extent to which the main theories of island biology are applicable to these systems: species–area and species–isolation relationships, community composition, evolutionary radiations, and the extent of endemism and genetic diversity. In the third and final part, I suggest a new conceptual framework within which to classify and study the biology of ILS, as well as practical future research directions. I conclude that the term ‘biological island’ is a multi‐faceted concept, loosely related to its geographical definition. As ILS are often less isolated than true islands, and their biological patterns are only partly similar to those of true islands (and even this is true only for some ILS) the use of the term ‘island’ to describe any isolated habitat is therefore inappropriate.     

Are legislative frameworks in Canada and Ontario up to the task of addressing invasive alien species?

As a signatory to the international Convention on Biological Diversity (CBD), Canada has committed to prevent, control, and eradicate invasive alien species (IAS). Yet, despite developing policy on biodiversity and IAS, the federal government has been criticized for its inaction on biological invasions over the past decade. In Canada’s most populous province, Ontario, similar concerns have been raised about the provincial government’s approach to dealing with IAS. The ongoing criticism of government response suggests that an effective legislative framework to guide and coordinate action on IAS may be lacking in Canada. In this paper, we examined how well existing legislation at the federal and Ontario levels addresses IAS threats, and thus contributes to CBD commitments. We reviewed a total of 98 pieces of legislation, comprised of 55 federal acts, two federal omnibus bills, and 41 Ontario acts. Of these, 20 federal and 12 Ontario acts were found to cover IAS either intentionally or incidentally, but IAS was not the central focus of most legislation. No consistent terminology existed across legislation referring to IAS, further highlighting a lack of focus on the issue. Legislation on IAS was administered by several different ministries both federally and in Ontario, but coordination of action among agencies was not explicitly addressed in laws and regulations. While many acts provided broad powers of enforcement, most provisions were not directly linked to IAS prevention and management. In general, Canada’s legislative framework on IAS is fragmented, and this complicates the development of a coordinated approach to the problem.