Twenty years of numerical syntaxonomy

The development of numerical syntaxonomy during its first 20 yr is reviewed. The use of methods of numerical classification and ordination is the dominating feature of the development. National and local phytosociological data banks were established, large data sets handled and many important vegetation monographs were methodically based on multivariate data analysis. Particularly the development in Italy, the Netherlands, Czechoslovakia, and Sweden contributed to new theoretical elements of numerical syntaxonomy. Ordination became a common tool of searching for reticulate synsystematic relations between community types. The most popular ordination techniques have been Principal Components Analysis and Detrended Correspondence Analysis. Hierarchical agglomerative techniques of clustering still prevail in classification, although the divisive strategy of TWINSPAN has also become an effective tool for phytosociological clustering and table sorting. Extensive program packages, also for personal computers have now become standard equipment for many vegetation scientists.     

Genetic determination of the mitochondrial adenine nucleotide translocation system and ITS role in the eukaryotic cell

On integrating experimental data published previously, the following picture of the mitochondrial adenine nucleotide (AdN) translocation system is being presented: 1. The AdN translocation system serves not only to transport ATP synthesized within mitochondria into the cytosol but also to transport cytosolic ATP into the mitochondria when oxidative phosphorylation is not functioning. 2. The AdN translocator is coded for by nuclear genes and the mitochondrial protein synthesis is not involved in its formation. 3. The AdN translocation system must be preserved and functioning even in cells which could dispense with oxidative phosphorylation. It assures appropriate concentrations of intramitochondrial ATP. 4. The intramitochondrial ATP is required for normal replication of mitochondrial DNA. Tis supports the view that the mitochondrion is a self-replicating semi-autonomous organelle. 5. The appropriate concentration of ATP must be present in mitochondria to make possible cell growth or multiplication. This points to a direct or indirect role of mitochondria in the control of cell proliferation.     

Development of a 16S rRNA gene-based prototype microarray for the detection of selected actinomycetes genera

Actinomycetes are known for their secondary metabolites, which have been successfully used as drugs in human and veterinary medicines. However, information on the distribution of this group of Gram-positive bacteria in diverse ecosystems and a comprehension of their activities in ecosystem processes are still scarce. We have developed a 16S rRNA-based taxonomic microarray that targets key actinomycetes at the genus level. In total, 113 actinomycete 16S rRNA probes, corresponding to 55 of the 202 described genera, were designed. The microarray accuracy was evaluated by comparing signal intensities with probe/target-weighted mismatch values and the Gibbs energy of the probe/target duplex formation by hybridizing 17 non-actinomycete and 29 actinomycete strains/clones with the probe set. The validation proved that the probe set was specific, with only 1.3% of false results. The incomplete coverage of actinomycetes by a genus-specific probe was caused by the limited number of 16S rRNA gene sequences in databases or insufficient 16S rRNA gene polymorphism. The microarray enabled discrimination between actinomycete communities from three forest soil samples collected at one site. Cloning and sequencing of 16S rRNA genes from one of the soil samples confirmed the microarray results. We propose that this newly constructed microarray will be a valuable tool for genus-level comparisons of actinomycete communities in various ecological conditions.     

Genetic Mapping in the Lignin-Degrading Basidiomycete Phanerochaete chrysosporium

A method of meiotic segregation analysis based on recombinant selection in the homothallic basidiomycete Phanerochaete chrysosporium was developed. Using this method, we were able to reveal linkage relationships and to estimate recombination frequencies between seven mutations to auxotrophy. We detected two linkage groups, the first containing four and the second three of the seven mapped mutations.     

Almost half of the RTX domain is dispensable for complement receptor 3 binding and cell-invasive activity of the Bordetella adenylate cyclase toxin

The whooping cough agent Bordetella pertussis secretes an adenylate cyclase toxin (CyaA) that through its large carboxy-proximal Repeat-in-ToXin (RTX) domain binds the complement receptor 3 (CR3). The RTX domain consists of five blocks (I–V) of characteristic glycine and aspartate-rich nonapeptides that fold into five Ca²⁺-loaded parallel β-rolls. Previous work indicated that the CR3-binding structure comprises the interface of β-rolls II and III. To test if further portions of the RTX domain contribute to CR3 binding, we generated a construct with the RTX block II/III interface (CyaA residues 1132–1294) linked directly to the C-terminal block V fragment bearing the folding scaffold (CyaA residues 1562–1681). Despite deletion of 267 internal residues of the RTX domain, the Ca²⁺-driven folding of the hybrid block III/V β-roll still supported formation of the CR3-binding structure at the interface of β-rolls II and III. Moreover, upon stabilization by N- and C-terminal flanking segments, the block III/V hybrid-comprising constructs competed with CyaA for CR3 binding and induced formation of CyaA toxin-neutralizing antibodies in mice. Finally, a truncated CyaAΔ_1295-1561 toxin bound and penetrated erythrocytes and CR3-expressing cells, showing that the deleted portions of RTX blocks III, IV, and V (residues 1295–1561) were dispensable for CR3 binding and for toxin translocation across the target cell membrane. This suggests that almost a half of the RTX domain of CyaA is not involved in target cell interaction and rather serves the purpose of toxin secretion.     

The sacredness of human life

Christian De Duve''s decision to voluntarily pass away gives us a pause to consider the value and meaning of death. Biologists have much to contribute to the discussion of dying with dignity.Christian de Duve''s voluntary passing away on 4 May 2013 could be seen as the momentous contribution of an eminent biologist and Nobel laureate to the discussion about ‘last things''. In contrast to his fellow scientists Ludwig Boltzmann and Allan Turing, who had made a deliberate choice to end their life in a state of depression and despair, de Duve “left with a smile and a good-bye”, as his daughter told a newspaper.What is the value and meaning of life? Is death inevitable? Should dying with dignity become an inalienable human right? Theologians, philosophers, doctors, politicians, sociologists and jurists have all offered their answers to these fundamental questions. The participation of biologists in the discussion is long overdue and should, in fact, dominate the discourse.We can start from de Duve''s premise—expressed as a subtitle of his book Cosmic Dust—that life is a cosmic imperative; a phenomenon that inevitably takes place anywhere in the universe as permitted by appropriate physicochemical conditions. Under such conditions, the second law of thermodynamics rules—prebiotic organic syntheses proceed, matter self-organizes into more complex structures and darwinian evolution begins, with its subsequent quasi-random walks towards increasing complexity. The actors of this cosmic drama are darwinian individuals—cells, bodies, groups and species—who strive to maintain their structural integrity and to survive as entities. By virtue of the same law, their components undergo successive losses of correlation, so that structures sustain irreparable damage and eventually break down. Because of this ‘double-edge'' of the second law, life progresses in cycles of birth, maturation, ageing and rejuvenation.Death is the inevitable link in this chain of events. ‘The struggle for existence'' is very much the struggle for individual survival, yet it is the number of offspring—the expression of darwinian fitness—that ultimately counts. Darwinian evolution is creative, but its master sculptor is death.Humans are apparently the only species endowed with self-consciousness and thereby a strongly amplified urge to survive. However, self-consciousness has also made humans aware of the existence of death. The clash between the urge for survival and the awareness of death must have inevitably engendered religion, with its delusion of an existence after death, and it might have been one of the main causes of the emergence of culture. Culture divides human experience into two parts: the sacred and the profane. The sacred constitutes personal transcendence: the quest for meaning, the awe of mystery, creativity and aesthetic feelings, the capacity for boundless love and hate, the joy of playing, and peaks of ecstasy. The psychologist Jonathan Haidt observed in his book The Righteous Mind: Why Good People Are Divided by Politics and Religion that “The great trick that humans developed at some point in the last few hundred thousand years is the ability to circle around a tree, rock, ancestor, flag, book or god, and then treat that thing as sacred. People who worship the same idol can trust one another, work as a team and prevail over less cohesive groups.” He considers sacredness as crucial for understanding morality. At present, biology knows almost nothing about human transcendence. Our ignorance of the complexity of human life bestows on it both mystery and sacredness.The religious sources of Western culture, late Judaism and Christianity, adopted Plato''s idea of the immortality of the human soul into their doctrines. The concept of immortality and eternity has continued to thrive in many secular versions and serves as a powerful force to motivate human creativity. Yet, immortality is ruled out by thermodynamics, and the religious version of eternal life in continuous bliss constitutes a logical paradox—eternal pleasure would mean eternal recurrence of everything across infinite time, with no escape; Heaven turned Hell. It is not immortality but temporariness that gives human life its value and meaning.There is no ‘existence of death''. Dying exists, but death does not. Death equals nothingness—no object, no action, no thing. Death is out of reach to human imagination, the intentionality of consciousness—its directedness towards objects—does not allow humans to grasp it. Death is no mystery, no issue at all—it does not concern us, as the philosopher Epicurus put it. The real human issue is dying and the terror of it. We might paraphrase Michel Montaigne''s claim that a mission of philosophy is to learn to die, and say that a mission of biology is to teach to die. Biology might complement its research into apoptosis—programmed cell death—by efforts to discover or to invent a ‘mental apoptosis''. A hundred years ago, the micro-biologist Ilya Mechnikov envisaged, in his book Essais Optimistes, that a long and gratifying personal life might eventually reach a natural state of satiation and evoke a specific instinct to withdraw, similar to the urge to sleep. Biochemistry could assist the process of dying by nullifying fear, pain and distress.In these days of advanced healthcare and technologies that can artificially extend the human lifespan, dying with dignity should become the principal concern of all humanists, not only that of scientists. It would therefore be commendable if Western culture could abandon the fallacy of immortality and eternity, whilst Oriental and African cultures ought to be welcomed to the discussion about the ‘last things''. Dying with dignity will become the ultimate achievement of a dignified life.     

Back from the Brink: The Holocene History of the Carpathian Barbel Barbus carpathicus

As a result of specific adaptations and habitat preferences strongly rheophilic fish species may show high levels of endemism. Many temperate rheophilic fish species were subjected to a series of range contractions during the Pleistocene, and then successfully expanded during the Holocene, colonising previously abandoned areas. The Carpathian barbel (Barbus carpathicus Kotlík, Tsigenopoulos, Ráb et Berrebi 2002) occurs in the montane streams in three basins of the main Central European rivers in the northern part of the Carpathian range. We used genetic variation within 3 mitochondrial and 9 microsatellite loci to determine a pattern of postglacial expansion in B. carpathicus. We found that overall genetic variation within the species is relatively low. Estimate of time to the most recent common ancestor (tMRCA) of mitochondrial sequences falls within the Holocene. The highest levels of genetic variation found in upper reaches of the Tisa river in the Danube basin suggest that glacial refugia were located in the south-eastern part of the species range. Our data suggest that the species crossed different watersheds at least six times as three genetically distinct groups (probably established in different expansion episodes) were found in northern part of the species range. Clines of genetic variation were observed in both the Danube and Vistula basins, which probably resulted from subsequent bottlenecks while colonizing successive habitats (south eastern populations) or due to the admixture of genetically diverse individuals to a previously uniform population (Vistula basin). Therefore, B. carpathicus underwent both demographic breakdowns and expansions during the Holocene, showing its distribution and demography are sensitive to environmental change. Our findings are important in the light of the current human-induced habitats alterations.     

Importance of plant integrity in crop research,breeding, and production

Plant integrity looks like a “very easy and expanded topic,” but the reality is totally different. Thanks to the very high specialization of scientists, we are losing a holistic view of plants and are making mistakes in our research due to this drawback. It is necessary to sense a plant in their whole complexity—in both roots and shoot, as well as throughout their life cycles. Only such an integrated approach can allow us to reach correct interpretations of our experimental results.