Rolled liverwort mats explain major Prototaxites features: Response to commentaries

In volume 97(2) of the American Journal of Botany (pp. 268-275), we published an article entitled "Structural, physiological, and stable carbon isotopic evidence that the enigmatic Paleozoic fossil Prototaxites formed from rolled liverwort mats". Here, we respond to a letter and a commentary on our article in the present issue, welcoming this opportunity to continue the scientific dialogue about an issue that has long been stimulating and controversial. For the reader's benefit, we first briefly describe the recent scholarly context of our article.     

Domains in biological membranes

Our current view on biological membranes has gradually evolved from the influential fluid mosaic model of the early 1970s to a distinctively more complex picture. Biological membranes are now assumed to encompass multiple membrane domains and a plethora of protein-lipid and protein-protein interactions that compartmentalize and temporarily order what has originally been envisioned to be mostly random. In this minireview, we will first highlight some structural principles that govern membrane domain formation and permit a classification of membrane domains. We will then focus on the still controversial issue of lipid-based membrane domains, or lipid rafts, and discuss recent advances in detecting these enigmatic structures in living cells. Finally we will evaluate biochemical approaches to characterize lipid rafts and discuss their contribution to the emerging topic of lipid raft diversity     

Clusterin

Clusterin is an enigmatic glycoprotein with a nearly ubiquitous tissue distribution and an apparent involvement in biological processes ranging from mammary gland involution to neurodegeneration in Alzheimer's disease. Its major form, a 75-80 kDa heterodimer, is secreted and present in physiological fluids, but truncated forms targeted to the nucleus have also been identified. Upregulation of clusterin mRNA and protein levels detected in diverse disease states and in in vitro systems have led to suggestions that it functions in membrane lipid recycling, in apoptotic cell death, and as a stress-induced secreted chaperone protein, amongst others. Recent studies of knockout mice have further complicated the picture by implicating clusterin in exacerbating neuronal death in hypoxia-ischemia. The question of whether clusterin is a multifunctional protein, or deploys a single primary function influenced by cellular context, remains a central issue continuing to stimulate interest in this unusual molecule.     

Lakes Hula and Agmon: destruction and creation of wetland ecosystems in northern Israel

A portion of the former Lake Hula wetland (northern Israel) was re-flooded in spring 1994 and the physical, chemical and biological developments within the resulting new lake and wetland complex (Agmon) was followed closely by a multi-disciplinary scientific team. The first three years of study relating to Lake Agmon are reported in this issue of Wetlands Ecology & Management. We provide in this paper a general background on the Lake Hula Draining Project in the 1950s and the recent re-flooding and creation of the Agmon wetland.     

Biological invasions in forest ecosystems: a global problem requiring international and multidisciplinary integration

The world’s forests are crucial biological resources that provide a variety of ecosystem services such as nutrient cycling and provisioning of resources to society. But forests are particularly affected by biological invasions, with regions around the world experiencing invasions by species from virtually every kingdom. Many of these species have severely disrupted forest ecosystem processes, thereby interrupting the provisioning of ecosystem services that societies depend upon. The problem of biological invasion in forests has many facets, and a large diversity of scientific disciplines addresses these issues. To make progress in solving the problems forest invasions pose, developing interdisciplinary collaborations is crucial because the causes of invasions and many of the measures for prevention or management require expertise in biology, economics, and social sciences. The goal of this special issue is to compile a series of articles summarizing various biological, sociological, and policy subject areas associated with forest invasions from a global perspective. These papers were prepared by the task force, “Forests and Biological Invasions,” organized by the International Union of Forest Research Organizations. Publication of this special issue is intended to advance the integration of scientific knowledge and development of solutions to this very serious and growing problem.     

On the nature of the species problem and the four meanings of 'species'

Present-day thought on the notion of species is troubled by a mistaken understanding of the nature of the issue: while the species problem is commonly understood as concerning the epistemology and ontology of one single scientific concept, I argue that in fact there are multiple distinct concepts at stake. An approach to the species problem is presented that interprets the term 'species' as the placeholder for four distinct scientific concepts, each having its own role in biological theory, and an explanation is given of the concepts involved. To illustrate how these concepts are commonly conflated, two widely accepted ideas on species are criticized: species individualism and species pluralism. I argue that by failing to distinguish between the four concepts and their particular roles in contemporary biological theory, these ideas stand in the way of a final resolution of the species problem.     

Biochemistry to the rescue: a ClC-2 auxiliary subunit provides a tangible link to leukodystrophy

ClC-2 is a broadly distributed chloride channel with an enigmatic neurophysiological function. In this issue of Neuron, Jeworutzki et al. (2012) use a biochemical approach to identify GlialCAM, a protein with a defined link to leukodystrophy, as a ClC-2 auxiliary subunit.     

Double helix of the journal Cytology and Genetics: 50 years later

This survey paper contains a brief analysis of publications included in the current issue of the scientific journal Cytology and Genetics dedicated to its 50th anniversary. These papers reflect scientific achievements of their authors in the field of genetics and cell biology and underline the potential of these two biological disciplines, forming the double helix of the journal.     

聚氨酯塑料的微生物降解

未被合理处置的废塑料污染已成为全球性的环境问题,探索塑料废弃物的无害化处理技术势在必行。近来,研究证实了自然界中存在可以降解塑料的微生物及酶。利用微生物或酶对废塑料进行生物处理成为可能。聚氨酯塑料(Polyurethane,PUR)是广泛应用的通用塑料之一,其废弃物量已占到所有废塑料总体积的30%。文中将PUR塑料发明应用70年来有关微生物降解的研究进行了全面综述,对PUR塑料降解真菌、细菌、降解基因与酶、降解产物及相关的生物处理技术系统等进行了总结与分析,并对实现PUR废塑料高效生物处理需解决的关键科学问题进行了展望。     

Biological responses to indoor air contaminants

Summary The scientific study of indoor air quality has been a topic for research in the last two decades; in the late 70's it became an issue of general public perception. The public perceptions have been such tremendous stimuli because they involve aspects of health and welfare (comfort and economics). Various biomedical studies were performed to evaluate adverse biological effects associated with ambient and occupational pollutants. However, it became obvious that humans were exposed more, on a temporal basis, to their normal indoor environments than they were either in the workplace or outside. Concern with biological contaminants was always an issue, but rarely examined indoors until recently. Biological responses to the indoor environment will be discussed in this paper.     

Pneumocystis: from a doubtful unique entity to a group of highly diversified fungal species

At the end of the 20th century the unique taxonomically enigmatic entity called Pneumocystis carinii was identified as a heterogeneous group of microscopic Fungi, constituted of multiple stenoxenic biological entities largely spread across ecosystems, closely adapted to, and coevolving in parallel with, mammal species. The discoveries and reasoning that led to the current conceptions about the taxonomy of Pneumocystis at the species level are examined here. The present review also focuses on the biological, morphological and phylogenetical features of Pneumocystis jirovecii, Pneumocystis oryctolagi, Pneumocystis murina, P. carinii and Pneumocystis wakefieldiae, the five Pneumocystis species described until now, mainly on the basis of the phylogenetic species concept. Interestingly, Pneumocystis organisms exhibit a successful adaptation enabling them to dwell and replicate in the lungs of both immunocompromised and healthy mammals, which can act as infection reservoirs. The role of healthy carriers in aerial disease transmission is nowadays recognized as a major contribution to Pneumocystis circulation, and Pneumocystis infection of nonimmunosuppressed hosts has emerged as a public health issue. More studies need to be undertaken both on the clinical consequences of the presence of Pneumocystis in healthy carriers and on the intricate Pneumocystis life cycle to better define its epidemiology, to adapt existing therapies to each clinical context and to discover new drug targets.     

Foreword: from the TRANSCRIPTOME conferences to the SYSTEMOSCOPE international consortium

This thematic issue issue of the Comptes rendus Biologies contains review articles, original papers and conference reports presented at the first two TRANSCRIPTOME conferences From Functional Genomics to Systems Biology and IMAGE Consortium Invitational workshops (Paris, November 2000 and Seattle, March 2002), and discussed during the inaugural meetings of the SYSTEMOSCOPE International Consortium (Paris, June 2003). We describe the founding principles, missions, working plan and policy for partnership and industrial development of SYSTEMOSCOPE to promote the study of the complexity of biological systems by integrating scientific, medical, ethical and economic issues in implementation of interdisciplinary projects for human health.     

Patent border wars: defining the boundary between scientific discoveries and patentable inventions

Drawing an appropriate boundary between unpatentable natural phenomena and patentable inventions is crucial in preventing the patent laws from unduly restricting access to fundamental scientific discoveries. Some would argue that, particularly in the U.S., patents are being issued that purport to claim a novel product or process but that, in effect, encompass any practical application of a fundamental biological principle. Examples include gene patents, which Congress is considering banning, and patents relating to biological correlations and pathways, such as the patents at issue in the headline-grabbing LabCorp v. Metabolite and Ariad v. Eli Lilly litigations. In view of the mounting concern, it seems likely that Congress and/or the courts will address the issue, and perhaps substantially shift the boundary.     

The many faces of biological individuality

Biological individuality is a major topic of discussion in biology and philosophy of biology. Recently, several objections have been raised against traditional accounts of biological individuality, including the objections of monism (the tendency to focus on a single individuality criterion and/or a single biological field), theory-centrism (the tendency to discuss only theory-based individuation), ahistoricity (the tendency to neglect what biologists of the past and historians of biology have said about biological individuality), disciplinary isolationism (the tendency to isolate biological individuality from other scientific and philosophical domains that have investigated individuality), and the multiplication of conceptual uncertainties (the lack of a precise definition of “biological individual” and related terms). In this introduction, I will examine the current philosophical landscape about biological individuality, and show how the contributions gathered in this special issue address these five objections. Overall, the aim of this issue is to offer a more diverse, unifying, and scientifically informed conception of what a biological individual is.     

Trends in biological control: public interest,international networking and research direction

We investigated trends in biological control to both capture its evolution and explore future opportunities. We examined recent changes in public interest, international networking and peer-reviewed research. A Google Trends analysis revealed that the popularity of biological control is decreasing in terms of search hits on the internet. This trend is potentially worrying for the biological control community, given that public interest tends to drive political decisions regarding regulatory processes and governmental funding of research. To examine patterns of international collaboration, we established the list of authors who published their work in the three main biological control journals from the early 1990s to 2016. International co-authorship has intensified and the biological control sector is increasingly characterized by multilateral collaboration. We surveyed papers published in BioControl and Biological Control over the last 25 years to identify research trends with respect to target pests, commodities, biological control agents and biological control approaches. Finally, we report that articles on biological control are published in the broad-based scientific journals Science and Nature on a regular basis. This reflects contributions that biological control research makes to scientific discussions in general. Our analyses revealed a thriving scientific discipline with several major research trends in arthropod, plant pathogen and weed biological control.     

Microbial production of vitamin B12

One of the most alluring and fascinating molecules in the world of science and medicine is vitamin B12 (cobalamin), which was originally discovered as the anti pernicious anemia factor and whose enigmatic complex structure is matched only by the beguiling chemistry that it mediates. The biosynthesis of this essential nutrient is intricate, involved and, remarkably, confined to certain members of the prokaryotic world, seemingly never have to have made the eukaryotic transition. In humans, the vitamin is required in trace amounts (approximately 1 microg/day) to assist the actions of only two enzymes, methionine synthase and (R)-methylmalonyl-CoA mutase; yet commercially more than 10 t of B12 are produced each year from a number of bacterial species. The rich scientific history of vitamin B12 research, its biological functions and the pathways employed by bacteria for its de novo synthesis are described. Current strategies for the improvement of vitamin B12 production using modern biotechnological techniques are outlined.     

Thinking Outside the Synapse: Glycine at Extrasynaptic NMDA Receptors

In this issue, Papouin et?al. show that glycine is the endogenous coagonist for extrasynaptic NMDA receptors (NMDARs), unlike at synapses where the coagonist is d-serine. By enzymatically degrading endogenous glycine, they begin to address the enigmatic physiological and pathological roles for extrasynaptic NMDARs.     

N-acetylation and ubiquitin-independent proteasomal degradation of p21(Cip1)

Expression of the CDK inhibitor p21(Cip1) is tightly regulated by signals that control cell division. p21 is an unstable protein that is degraded by the proteasome; however, the pathway that leads to proteasomal degradation of p21 has proven to be enigmatic. An important issue is whether proteasomal degradation of p21 occurs independently of ubiquitylation or, alternatively, whether ubiquitylation on its N terminus is crucial. We resolve this uncertainty by showing that endogenous cellular p21 is completely acetylated at its amino terminus and is therefore not a substrate for N-ubiquitylation. We further show that inactivation of essential components of the ubiquitylation machinery does not directly impact endogenous p21 degradation. Our results underscore the importance of N-acetylation in restricting N-ubiquitylation and show, in particular, that ubiquitylation of endogenous p21 either at internal lysines or on the N terminus is unlikely to control its degradation by the proteasome.     

Fortifying the link between SIRT1, resveratrol, and mitochondrial function

The molecular mechanisms behind the health benefits of resveratrol remain enigmatic and controversial. In this issue of Cell Metabolism, Price et al. establish a clear chemical-genetic connection between SIRT1 and resveratrol, providing strong evidence that SIRT1 is critical for resveratrol to stimulate mitochondrial biogenesis and a switch toward oxidative muscle fibers (Price et al., 2012).     

IPBES评估报告对全球生物多样性保护的影响——以美国传粉者保护政策为例

作为生物多样性领域首个政府间、多学科、跨领域的综合性科学政策平台, 联合国生物多样性和生态系统服务政府间科学-政策平台(The Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services, IPBES)将会对全球生物多样性保护及其他领域产生重要影响。本文通过分析美国传粉者保护政策的制定和实施过程, 获得了生物多样性相关保护政策的制定为科学评估-政府关注-出台限制性政策措施的过程和模式。基于IPBES 2016年发布《传粉者、传粉与粮食生产评估报告》(The Assessment Report on Pollinators, Pollination and Food Production)的事实, 推测IPBES交付品可能促进对新烟碱类农药产业和蜂产品尤其是野生蜂产品交易限制性政策的产生。并进一步分析了IPBES交付品可能在全球以及我国生物多样性保护及其相关领域带来的影响, 比如可能通过促进生物多样性领域的科学评估, 进一步主流化生物多样性保护问题, 促使生物多样性保护成为重要的政治议题。本文旨在为我国建立生物多样性保护的适应性政策提供科学支持。