Reinforcing the foundations of ornithological nomenclature: Filling the gaps in Sherborn’s and Richmond’s historical legacy of bibliographic exploration

Due to its public popularity, ornithology has a huge corpus of scientific publication for a relatively small number of species. Although there are global checklists of currently recognised taxa, there has been only limited, mainly individual, effort to build a nomenclatural database that the science of ornithology deserves. This is especially true in relation to concise synonymies. With the arrival of ZooBank and the Biodiversity Heritage Library, the time has come to develop synonymies and to add fuller bibliographic detail to databases. The preparation for both began at the start of the 20^th century with extensive work by Sherborn and Richmond. I discuss their legacy, offer notes on significant work since then, and provide suggestions for what remains to be done. To make solid the foundations for ornithological nomenclature and taxonomy, especially for synonymies, ornithologists will need to collaborate much more and contribute to the digital infrastructure.     

Zoological nomenclature in the century of extinctions: priority vs. ‘usage’

Our epoch is a crucial one for scientific knowledge of the organisms that live on our planet. The combination of the biodiversity crisis and the taxonomic gap results in taxonomic urgency. In this context, great attention should be paid to the nomenclatural rules helping taxonomists in their urgent task, rather than diverting their time and energy to secondary questions or debates. In zoology, the new criterion of ‘prevailing usage’, introduced in the 1999 edition of the Code of nomenclature to ‘protect’ some nomina, raises four kinds of problems: (1) it weakens the binding value and strength of the Code, thus indirectly bringing support to the development of alternative nomenclatural systems; (2) it encourages personal debates among taxonomists, giving undue importance to the ‘argument of authority’ in nomenclatural decisions; (3) it sends a wrong message to non-taxonomists as regards completion of the taxonomic work; (4) it acts as a threat against natural history museums, in devaluing onomatophores (type specimens), the conservation of which is one of their major ‘visible’ functions. In conclusion, it is suggested that ‘protection’ of some nomina ‘threatened’ by rules of the Code should be limited strictly to nomina well-known outside the small world of systematics. This would require new rules for the Code to clearly define categories of usage on the basis of objective criteria.     

R. J. Gordon’s Discovery of the Spotted Hyena’s Extraordinary Genitalia in 1777

In the history of zoology the English anatomist Morrison Watson (1845–1885) is considered to be the discoverer of the masculinized sexual organs of the spotted hyena. Beginning in 1877, Watson had published a series of anatomical studies on the spotted hyena (Watson, 1877, 1878, 1881, Watson and Young, 1879), in which he, in which he for the first time made public the anatomical peculiarities of the female spotted hyena’s genitalia. This scientific achievement is well documented. But now we can also state that a hundred years before Watson the Dutch amateur zoologist Robert Jacob Gordon (1743–1795), while serving in the Scots Brigades at the Cape of Good Hope, had already made the same discovery and merely unfortunate personal circumstances prevented publication. During his stay at the Cape, Gordon had studied spotted hyenas intensively and recorded his observations in accurate drawings and comments. These drawings have been preserved as part of a large collection of animal drawings entitled Gordon Atlas. With his discovery, Gordon actually was the first to provide empirical evidence of a “curious and inexplicable case of dimorphism” (Darwin on a beetle) in mammalians, long before étienne Geoffrey Saint-Hilaire (Cours de l’histoire naturelle des mammifères, 1829) started examining masculinized sexual organs in the mole or Darwin recognized the importance of sexual dimorphism (Descent of Man, 1871). In this paper we reproduce for the first time all hyena drawings from the Gordon Atlas, including Gordon’s handwritten notes in the margins in the original Dutch and in translation. Additionally, we briefly delineate the knowledge about the South African spotted hyena in Gordon’s time and indicate that we doubt Watson’s explanation for the age-old confusion about the hyena.     

Itinerary of Truman G. Yuncker’s expeditions

Many of the systematically and historically valuable collections in the DePauw University Herbarium (DPU), Greencastle, Indiana, were made by Truman G. Yuncker during his numerous expeditions. He collected in large, and until then unexplored, areas of Honduras, and undertook several expeditions to islands in the South Pacific (Manua, Niue, and Tonga) and Hawaii. In his late years he collected in the West Indies and in Brazil. His extensive collections ofCuscuta (Cuscutaceae) and Piperaceae each became among the largest in the world. In this article an itinerary of his expeditions is presented.     

Psychological Analysis of M.A. Vrubel’s Creative Potential

The author motivates his analysis by a general need for creativity as a precondition of human survival. He assumes that creativity and ‘talent’ is connected with such factors as supportive social conditions, presence of constructive dissonance, certain level of consciousness, creating original products, creative strategies, and creative groups or ‘private laboratory’. vrublev’s biographical analysis divided his production into three thematic domains.     

Microscale’s relationship between Young’s modulus and tissue density. Prediction of displacements

The study presents an experimental verification of Wagner et al.’s relationship in microscale and proposes a modification of this relationship. For this purpose, 11 cubic specimens were microcomputed tomography scanned and mechanically tested with the displacement full-field measurements using a digital image correlation system. Then, numerical simulations of the compression tests were performed using a finite elements method. The Young’s modulus distributions assigned to the finite elements models were calculated using both of Wagner et al.’s relationships: original and modified. Comparison of the experimental and numerical results indicated the accuracy of numerical solutions for both relationships.     

Sherborn’s Index Animalium: New names,systematic errors and availability of names in the light of modern nomenclature

This study is aimed to shed light on the reliability of Sherborn’s Index Animalium in terms of modern usage. The AnimalBase project spent several years’ worth of teamwork dedicated to extracting new names from original sources in the period ranging from 1757 to the mid-1790s. This allowed us to closely analyse Sherborn’s work and verify the completeness and correctness of his record. We found the reliability of Sherborn’s resource generally very high, but in some special situations the reliability was reduced due to systematic errors or incompleteness in source material. Index Animalium is commonly used by taxonomists today who rely strongly on Sherborn’s record; our study is directed most pointedly at those users. We recommend paying special attention to the situations where we found that Sherborn’s data should be read with caution.In addition to some categories of systematic errors and mistakes that were Sherborn’s own responsibility, readers should also take into account that nomenclatural rules have been changed or refined in the past 100 years, and that Sherborn’s resource could eventually present outdated information. One of our main conclusions is that error rates in nomenclatoral compilations tend to be lower if one single and highly experienced person such as Sherborn carries out the work, than if a team is trying to do the task. Based on our experience with extracting names from original sources we came to the conclusion that error rates in such a manual work on names in a list are difficult to reduce below 2–4%. We suggest this is a natural limit and a point of diminishing returns for projects of this nature.     

Codon Bias Patterns of E. coli’s Interacting Proteins

Synonymous codons, i.e., DNA nucleotide triplets coding for the same amino acid, are used differently across the variety of living organisms. The biological meaning of this phenomenon, known as codon usage bias, is still controversial. In order to shed light on this point, we propose a new codon bias index, CompAI, that is based on the competition between cognate and near-cognate tRNAs during translation, without being tuned to the usage bias of highly expressed genes. We perform a genome-wide evaluation of codon bias for E.coli, comparing CompAI with other widely used indices: tAI, CAI, and Nc. We show that CompAI and tAI capture similar information by being positively correlated with gene conservation, measured by the Evolutionary Retention Index (ERI), and essentiality, whereas, CAI and Nc appear to be less sensitive to evolutionary-functional parameters. Notably, the rate of variation of tAI and CompAI with ERI allows to obtain sets of genes that consistently belong to specific clusters of orthologous genes (COGs). We also investigate the correlation of codon bias at the genomic level with the network features of protein-protein interactions in E.coli. We find that the most densely connected communities of the network share a similar level of codon bias (as measured by CompAI and tAI). Conversely, a small difference in codon bias between two genes is, statistically, a prerequisite for the corresponding proteins to interact. Importantly, among all codon bias indices, CompAI turns out to have the most coherent distribution over the communities of the interactome, pointing to the significance of competition among cognate and near-cognate tRNAs for explaining codon usage adaptation. Notably, CompAI may potentially correlate with translation speed measurements, by accounting for the specific delay induced by wobble-pairing between codons and anticodons.     

Young’s modulus of elasticity of Schlemm’s canal endothelial cells

Schlemm’s canal (SC) endothelial cells are likely important in the physiology and pathophysiology of the aqueous drainage system of the eye, particularly in glaucoma. The mechanical stiffness of these cells determines, in part, the extent to which they can support a pressure gradient and thus can be used to place limits on the flow resistance that this layer can generate in the eye. However, little is known about the biomechanical properties of SC endothelial cells. Our goal in this study was to estimate the effective Young’s modulus of elasticity of normal SC cells. To do so, we combined magnetic pulling cytometry of isolated cultured human SC cells with finite element modeling of the mechanical response of the cell to traction forces applied by adherent beads. Preliminary work showed that the immersion angles of beads attached to the SC cells had a major influence on bead response; therefore, we also measured bead immersion angle by confocal microscopy, using an empirical technique to correct for axial distortion of the confocal images. Our results showed that the upper bound for the effective Young’s modulus of elasticity of the cultured SC cells examined in this study, in central, non-nuclear regions, ranged between 1,007 and 3,053 Pa, which is similar to, although somewhat larger than values that have been measured for other endothelial cell types. We compared these values to estimates of the modulus of primate SC cells in vivo, based on images of these cells under pressure loading, and found good agreement at low intraocular pressure (8–15 mm Hg). However, increasing intraocular pressure (22–30 mm Hg) appeared to cause a significant increase in the modulus of these cells. These moduli can be used to estimate the extent to which SC cells deform in response to the pressure drop across the inner wall endothelium and thereby estimate the extent to which they can generate outflow resistance.     

Composition and properties of pectin polysaccharides of St. John’s wort Hypericum Perforatum L.

Three fractions of acidic water-soluble polysaccharides (concentration of glucuronic acid 10?C65%) were obtained from the above-ground part of St. Johns wort Hypericum perforatum L. by serial extraction with water and 0.7% aqueous solution of ammonium oxalate. Enzymatic hydrolysis of these polysaccharides using endo-polygalacturonase indicates that their carbohydrate chains contain the units of galacturone formed by 1,4-??-linked residues of non-substituted D-galacturonic acid. The extracted polysaccharides have been purified by means of gel filtration. It has been shown that water-soluble polysaccharides obtained by extraction with water manly contain the residues of galactose, mannose, glucose, and arabinose (the concentration of glucuronic acid being 10?C27%) while the polysaccharide fraction extracted using 0.7% aqueous solution of ammonium oxalate is presented by pectin polysaccharides. Only the residues of galacturonic acid (55?C72%) have been identified among glucuronic acids in its composition using chromatography/mass spectrometry of trimethylsilyl derivatives. In addition, this fraction contains the residues of the neutral monosaccharides which are typical for pectins: arabinoses, galactoses, rhamnoses, and glucose; there are also minor concentrations of residues of xylose and mannose. IR spectra of pectin polysaccharides of St. John??s wort have absorption bands in the ranges 1740, 1640?C1620, 1236?C1200, and 1200?C1000 cm^?1 which are typical for pectins. It has been demonstrated that aqueous solutions of pectin polysaccharides of St. John??s wort (2 mg/mL) have pronounced antioxidant activity (44% of the activity of trolox taken for 100%).     

The 70th anniversary of E.N. Pavlovsky’s concept of natural nidality of human diseases

The concept of the natural nidality of human diseases has significantly changed during the last 70 years, but its essence is preserved. Many “new” infections with natural foci were discovered and their geographical distribution was investigated in detail, and the classification of natural foci was developed. It has been established that epidemic features of transmissible infections depend mainly on types of parasitism of insect, tick and mite vectors.     

The Impact of Lamarck’s Theory of Evolution Before Darwin’s Theory

This paper analyzes the impact that Lamarckian evolutionary theory had in the scientific community during the period between the advent of Zoological Philosophy and the publication Origin of Species. During these 50 years Lamarck’s model was a well known theory and it was discussed by the scientific community as a hypothesis to explain the changing nature of the fossil record throughout the history of Earth. Lamarck’s transmutation theory established the foundation of an evolutionary model introducing a new way to research in nature. Darwin’s selectionist theory was proposed in 1859 to explain the origin of species within this epistemological process. In this context, Charles Lyell’s Principles of Geology and Auguste Comte’s Cours de Philosophie Positive appear as two major works for the dissemination of Lamarck’s evolutionary ideology after the death of the French naturalist in 1829.     

Schweingruber’s cosmos of inspiration

Born 29^th February 1936 near Bern, Switzerland, Fritz Hans Schweingruber worked as a teacher until 1965, obtained a PhD in botany from the University of Basel in 1972 (where he also obtained a Professorship in 1976), and started his lifelong career at the Swiss Federal Research Institute WSL in Birmensdorf right afterwards. Fritz developed a dendrochronological network across much of the Northern Hemisphere, expanded wood (xylem) science beyond forests, implemented wood anatomical techniques into dendroecology and paleoclimatology, and enthusiastically trained thousands of students, of which hundreds remained actively involved in the still emerging field of tree-ring research. Though Fritz died 7^th January 2020 after an extraordinary academic career, his intellectual legacy will continue to inspire scholars around the world.     

Pathogenesis of parkinson’s disease

Parkinson's disease (PD) is caused by the degeneration of dopaminergic neurons of substantia nigra projecting to striatum. The cause of idiopathic PD is obscure, and most cases are sporadic. It is widely accepted that there is a genetic component of the disease, and the earlier the age of onset, the greater the likelihood that genetic factors play a dominant role. Oxidative stress of the substantia nigra seems to contain the driving force for neurodegeneration, leading to a destructive "toxic cycle." The most prevalent therapy is levodopa administration, but it is not efficacious after several years of treatment. Several alternative therapies are currently being explored, such as neuroprotective approaches. Compounds with potentially neuroprotective efficacy such as selegiline, dopamine agonists, riluzole, creatine, and coenzyme Q10 are currently being tested. Trophic factors represent another class of neuroprotective compounds, but their intracerebral administration is difficult to achieve. In this respect, a potentially useful therapeutic approach is grafting cell vectors that release trophic molecules that stimulate regeneration in the damaged nigrostriatal system. Promising results have been obtained with fibroblasts engineered to secrete glial cell line-derived neurotrophic factor (GDNF) or brain-derived neurotrophic factor (BDNF) or viral vectors expressing GDNF. We have tested the suitability of intrastriatal grafts of chromaffin cells obtained from the Zuckerkandl's organ, which exert beneficial effects in parkinsonian rats, and release trophic factors such as GDNF and transforming growth factor-beta1 (TGF-beta1).     

Influence of nitrogen on the production of hypericins by St. John’s wort

The effect of nitrogen supply on the production of ‘hypericins’ (hypericin and pseudohypericin) in leaves of St. John’s wort (Hypericum perforatum L.) was examined with plants grown in sand culture and soil. In sand culture, 56-d growth of St. John’s wort plants with decreased nitrogen levels resulted in increased production of hypericins in leaves. A short-term low nitrogen stress in sand culture also resulted in increased production of leaf hypericins. While growth in a low nitrogen-containing soil resulted in elevated levels of hypericins, their production was decreased by supplementation of the soil with additional nitrogen. Increased production of hypericins in St. John’s wort leaves did not require the nitrogen supply to be decreased to levels that resulted in nitrogen deficiency symptoms. Moreover, alteration in the production of leaf hypericins occurring with changes in nitrogen supply did not alter the concentration ratio of pseudohypericin and hypericin. Increased production of leaf hypericins was not associated with any significant changes in the number of dark glands on the leaves and only a weak correlation was observed between leaf dark gland number and levels of leaf hypericins. These results are discussed in terms of the biochemistry of naphthodianthrone production by St. John’s wort plants and implications for growth environment effects during cultivated growth of this medicinal plant.