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.     

Breeding system of diploid sexuals within the Ranunculus auricomus complex and its role in a geographical parthenogenesis scenario

The larger distribution area of asexuals compared with their sexual relatives in geographical parthenogenesis (GP) scenarios has been widely attributed to the advantages of uniparental reproduction and polyploidy. However, potential disadvantages of sexuals due to their breeding system have received little attention so far. Here, we study the breeding system of five narrowly distributed sexual lineages of Ranunculus notabilis s.l. (R. auricomus complex) and its effects on outcrossing, inbreeding, female fitness, and heterozygosity. We performed selfing and intra‐ and interlineage crossings by bagging 481 flowers (59 garden individuals) followed by germination experiments. We compared seed set and germination rates, and related them to genetic distance and genome‐wide heterozygosity (thousands of RADseq loci). Selfings (2.5%) unveiled a significantly lower seed set compared with intra‐ (69.0%) and interlineage crossings (69.5%). Seed set of intra‐ (65%) compared to interpopulation crossings (78%) was significantly lower. In contrast, all treatments showed comparable germination rates (32%–43%). Generalized linear regressions between seed set and genetic distance revealed positive relationships in general and between lineages, and a negative one within lineages. Seed set was the main decisive factor for female fitness. Germination rates were not related to genetic distance at any level, but were positively associated with heterozygosity in interlineage crossings. Experiments confirmed full crossability and predominant outcrossing among sexual R. notabilis s.l. lineages. However, up to 5% (outliers 15%–31%) of seeds were formed by selfing, probably due to semi‐self‐compatibility in a multi‐locus gametophytic SI system. Less seed set in intrapopulation crossings, and higher seed set and germination rates from crossings of genetically more distant and heterozygous lineages (interlineage) indicate negative inbreeding and positive outbreeding effects. In GP scenarios, sexual species with small and/or isolated populations can suffer from decreased female fitness due to their breeding system. This factor, among others, probably limits range expansion of sexuals.     

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.     

Receptors for the neuropeptides,myoinhibitory peptide and SIFamide,in control of the salivary glands of the blacklegged tick Ixodes scapularis

Tick salivary glands are important organs that enable the hematophagous feeding of the tick. We previously described the innervation of the salivary gland acini types II and III by a pair of protocerebral salivary gland neurons that produce both myoinhibitory peptide (MIP) and SIFamide (?imo et al., 2009b). In this study we identified authentic receptors expressed in the salivary glands for these neuropeptides. Homology-based searches for these receptors in the Ixodes scapularis genome sequence were followed by gene cloning and functional expression of the receptors. Both receptors were activated by low nanomolar concentrations of their respective ligands. The temporal expression patterns of the two ligands and their respective receptors suggest that the SIFamide signaling system pre-exists in unfed salivary glands, while the MIP system is activated upon initiation of feeding. Immunoreactivity for the SIFamide receptor in the salivary gland was detected in acini types II and III, surrounding the acinar valve and extending to the basal region of the acinar lumen. The location of the SIFamide receptor in the salivary glands suggests three potential target cell types and their probable functions: myoepithelial cell that may function in the contraction of the acini and/or the control of the valve; large, basally located dopaminergic granular cells for regulation of paracrine dopamine; and neck cells that may be involved in the control of the acinar duct and its valve.     

Influence of the O-phosphorylation of serine, threonine and tyrosine in proteins on the amidic 15N chemical shielding anisotropy tensors

Density functional theory was employed to study the influence of O-phosphorylation of serine, threonine, and tyrosine on the amidic ¹⁵N chemical shielding anisotropy (CSA) tensor in the context of the complex chemical environments of protein structures. Our results indicate that the amidic ¹⁵N CSA tensor has sensitive responses to the introduction of the phosphate group and the phosphorylation-promoted rearrangement of solvent molecules and hydrogen bonding networks in the vicinity of the phosphorylated site. Yet, the calculated ¹⁵N CSA tensors in phosphorylated model peptides were in range of values experimentally observed for non-phosphorylated proteins. The extent of the phosphorylation induced changes suggests that the amidic ¹⁵N CSA tensor in phosphorylated proteins could be reasonably well approximated with averaged CSA tensor values experimentally determined for non-phosphorylated amino acids in practical NMR applications, where chemical surrounding of the phosphorylated site is not known a priori in majority of cases. Our calculations provide estimates of relative errors to be associated with the averaged CSA tensor values in interpretations of NMR data from phosphorylated proteins.