Bibliography of ‘molecular systematic’ studies of bryophytes. I. 1985–2000

A bibliography of all studies using characters of DNA sequences to address questions pertaining to the systematics of bryophytes are enumerated. In total 90 research articles are listed. These are arranged according to method of data gathering (Random or specific amplification) and the genomic source of the data analyzed (i.e., nuclear, chloroplastic or mitochondrial).     

The 1991–1992 rapid ecological assessment of Palau’s coral reefs

At the request of the Palau and US governments, a team of 30 scientists under the leadership of the Nature Conservancy completed a rapid ecological assessment (REA) of nearshore marine resources in Palau in 1992. The REA provided ecological input to Palau's ongoing master plan for economic development and identified 45 marine sites worthy of special protection. The REA relied on previous literature, 1992 aerial photography, interviews, and field observations. A combination of qualitative and quantitative techniques were used to assess stony corals, other reef invertebrates, reef and shore fishes, macroscopic algae, seagrasses, sea turtles and other marine organisms. The REA covered a variety of coral reef habitats including beaches, seagrass beds, fringing reefs, lagoons, passes, channels, reef holes, patch and pinnacle reefs, barrier reefs, atolls, submerged reefs, mangroves, and rock islands. Major stresses to Palau's coral reefs include sedimentation from soil erosion, overfishing, and damage from periodic storms and waves. Minor stresses include dredge-and fill activities, sewage pollution, anchor damage, tourism use, ship groundings, aquarium fish collecting, and minor crown-of-thorns (Acanthaster) infestations.     

Design,synthesis and evaluation of tacrine–flurbiprofen–nitrate trihybrids as novel anti-Alzheimer’s disease agents

To search for multifunctional anti-Alzheimer’s disease (AD) agents with good safety, the previously synthesized tacrine–flurbiprofen hybrids 1a and 1b were modified into tacrine–flurbiprofen–nitrate trihybrids 3a–h. These compounds displayed comparable or higher cholinesterase inhibitory activity relative to the bivalent hybrids. Compound 3a was the most potent, which released moderate NO, exerted blood vessel relaxative activity, and showed significant Aβ inhibitory effects whereas tacrine and flurbiprofen did not exhibit any Aβ inhibitory activity at the same dose. In addition, 3a was active in improving memory impairment in vivo. More importantly, the hepatotoxicity study showed that 3a was much safer than tacrine, suggesting it might be a promising anti-AD agent for further investigation.     

A harmony of illusions: clinical and experimental testing of Robert Koch’s tuberculin 1890–1900

One of Ludwik Fleck’s ideas about the development of scientific knowledge is that—once a system of interpretation is in place—the process that follows can be characterised as one of inertia: any new evidence comes under a strong pressure to be incorporated into the established frame. This can result in what Fleck called a harmony of illusions (Harmonie der Täuschungen) when contradictory evidence becomes almost invisible or is incorporated into the established frame only by huge efforts.The paper analyses early explanations of the tuberculin reaction as a case study of Fleck’s argument. For Robert Koch, who had presented tuberculin in 1890, the compound was supposed to be a diagnostic tool and a cure for tuberculosis. His conception of its effect was rather peculiar, but strictly in line with ideas on the pathogenesis of infectious diseases he had developed much earlier. After tuberculin was released in late 1890, whether Koch’s conception was convincing depended on the place that a given observer had in the medical world in late-nineteenth-century Germany. Inside Koch’s group, the status of the tuberculin reaction remained stable and tuberculin retained its value as a diagnostic and curative tool. On the other hand, observers from outside that thought collective, and in particular from clinical medicine, soon pointed to flaws in its conception. These critics developed a rather different picture of tuberculin as a mysterious and dangerous drug. No reconciliation followed and what we find instead in German medicine around the year 1900 is the presence of rather contradictory concepts and practices surrounding Koch’s wonder cure.     

Michurinist Biology in the People’s Republic of China, 1948–1956

Michurinist biology was introduced to China in 1948; granted a state supported monopoly in 1952; and reduced to parity with western genetics from 1956. The Soviets exported it through the propaganda agencies Sino Soviet Friendship Association (SSFA) and VOKS (Cultural Relations with Foreign Countries). China’s Ministry of Agriculture achieved broad public awareness and acceptance of Michurinist biology through a translation, publication, and Soviet guest speakers campaign – all managed by a team of agriculturalists led by Luo Tianyu, a veteran CCP (Communist Party) cadre. The campaign grew exponentially, but did not affect university or Chinese Academy of Sciences biology. Luo Tianyu’s failed attempt to force Michurinist biology on a Beijing university triggered its second stage: monopoly status and a ban on “Mendelist-Morganist” biology in teaching, research, and publication. The CCP Central Committee supported this policy believing that Michurinst biology would increase agricultural production for the forthcoming first Five Year Plan; whereas, western genetics had no practical value. Michurinist biology flourished at all levels of education, research, and science literature; Western genetics was completely shut down. This only began to change when the CCP Central Committee became wary of China’s dependency on Soviet technical expertise and failure to fully utilize that of China. Change was further promoted by significant attacks on Michurinist biology by Soviet and East German biologists. Soon, these developments informed China’s “genetics question,” which became a test case for larger questions about the definition of science and the relationship between scientists and the state. Under the guidance of Lu Dingyi’s Central Committee Propaganda Department, the CCP eventually decided that, henceforth, science controversies would only be resolved by the science community; and that monopolies or ideological orthodoxies would not be imposed on science. At the same time, the CCP rescinded Michurinist biology’s monopoly and the ban on western genetics. By the mid-1960s western genetics had successfully restored itself, largely due to the leadership of C. C. Tan, a former student of Dobzhansky. Michurinist biology’s presence shrank and it became marginalized.     

Timing of butterfly parasitization of a plant–ant–scale symbiosis

In the Southeast Asian tropics, Arhopala lycaenid butterflies feed on Macaranga ant-plants inhabited by Crematogaster (subgenus Decacrema) ants tending Coccus-scale insects. A recent phylogenetic study showed that (1) the plants and ants have been codiversifying for the past 20–16 million years (Myr), and that (2) the tripartite symbiosis was formed 9–7 Myr ago, when the scale insects became involved in the plant–ant mutualism. To determine when the lycaenids first parasitized the Macaranga tripartite symbiosis, we constructed a molecular phylogeny of the lycaenids that feed on Macaranga by using mitochondrial and nuclear DNA sequence data and estimated their divergence times based on the cytochrome oxidase I molecular clock. The minimum age of the lycaenids was estimated by the time-calibrated phylogeny to be 2.05 Myr, about one-tenth the age of the plant–ant association, suggesting that the lycaenids are latecomers that associated themselves with the pre-existing symbiosis of plant, ant, and scale insects.     

Armin von Tschermak-Seysenegg (1870–1952): Physiologist and Co-‘Rediscoverer’ of Mendel’s laws

The ‘rediscovery’ of Mendel’s laws in 1900 was a turning point in modern research of heredity/genetics. According to the traditional view, adopted and fostered by many textbooks of genetics, Mendel’s principles were presented in the first half of 1900 simultaneously and independently by three biologists (H. de Vries, C. Correns, E. v. Tschermak-Seysenegg). Having thus laid the foundations of further development, the ‘rediscovery’ continues to attract considerable interest. Since the 1950s, however, serious questions arose concerning both the chronology and specific conceptual achievement of the scientists involved. Not only the independence but also parallelism was analysed in the context of individual research programmes of these three scholars. The youngest of them, Erich v. Tschermak-Seysenegg, was even excluded from the list of ‘rediscoverers’. The aim of this paper is to use new archival evidence and approximate the contribution of the physiologist and ophthalmologist Armin von Tschermak-Seysenegg (1870–1952) to the events of 1900 and 1901.     

L’homme-lion d’Hohlenstein – Stadel

The fragments of the figurine called “lion-man” were found in 1939 in the cave of Hohlenstein-Stadel, in southwestern Germany. Joachim Hahn was the first to assemble the figure in 1969; the statuette was then restored between 1987 and 1988 in the workshops of the regional museum of Württemberg in Stuttgart. New excavations, conducted by the State Office for Cultural Heritage of Baden-Württemberg (Esslingen, Germany), were held in the same cave between 2009 and 2013. Then, hundreds of small fragments were found; some of them clearly belonged to the lion-man. Following these excavations, a second restoration was undertaken in the workshops of the State office of Cultural Heritage in 2012 and 2013. The Lion-Man, the tallest of the figures from the last Ice Age, got a new appearance. After the refitting of the fragments, a large part of the figurine has been completed.     

Dynamics of plant–pollinator–robber systems

Plant–pollinator–robber systems are considered, where the plants and pollinators are mutualists, the plants and nectar robbers are in a parasitic relation, and the pollinators and nectar robbers consume a common limiting resource without interfering competition. My aim is to show a mechanism by which pollination–mutualism could persist when there exist nectar robbers. Through the dynamics of a plant–pollinator–robber model, it is shown that (i) when the plants alone (i.e., without pollination–mutualism) cannot provide sufficient resources for the robbers’ survival but pollination–mutualism can persist in the plant–pollinator system, the pollination–mutualism may lead to invasion of the robbers, while the pollinators will not be driven into extinction by the robbers’ invasion. (ii) When the plants alone cannot support the robbers’ survival but persistence of pollination–mutualism in the plant–pollinator system is density-dependent, the pollinators and robbers could coexist if the robbers’ efficiency in translating the plant–robber interactions into fitness is intermediate and the initial densities of the three species are in an appropriate region. (iii) When the plants alone can support the robbers’ survival, the pollinators will not be driven into extinction by the robbers if their efficiency in translating the plant–pollinator interactions into fitness is relatively larger than that of the robbers. The analysis leads to an explanation for the persistence of pollination–mutualism in the presence of nectar robbers in real situations.     

Calculation of the Three-Dimensional Structures of Two Antigenic Sequences, Pro–Pro–Pro–Pro–Asn–Pro–Asn–Asp–Pro and Pro–Pro–Pro–Pro–Asn–Pro–Asn–Asp–Pro–Pro–Pro, of the Circumsporozoite Protein From a Malaria-Causing Plasmodium

Using the chain build-up procedure based on the program ECEPP, we have computed the lowest energy structures for two terminally blocked subsequences from the antigenic circumsporozoite protein of Plasmodium berghei, that is known to cause malaria in animals. The full antigenic sequence is an octapeptide proline-rich tandem repeat, (Pro–Pro–Pro–Pro–Asn–Pro–Asn–Asp)₂. We computed the structures for the first octapeptide plus one Pro from the second octapeptide, terminally blocked CH₃CO–Pro–Pro–Pro–Pro–Asn–Pro–Asn–Asp–Pro–NHCH₃ as well as the first octpeptide with an additional three Pro residues from the adjoining unit, i.e., CH₃CO–Pro–Pro–Pro–Pro–Asn–Pro–Asn–Asp–Pro–Pro–Pro–NHCH₃. We find that the first sequence adopts a number of different low energy structures, the most probable of which has a probability of occurrence of 56 %. Addition of two more Pro residues results in the adoption a single, unique lowest energy structure that has a probability of occurrence of over 95 % without solvation effects and 86 % when solvation effects are included in the calculations. We predict that this structure may be the one recognized as a major antigenic determinant.     

Mechanisms of the Effects of Crocin on Aggregation and Deposition of Aβ1–40 Fibrils in Alzheimer’s Disease

Alzheimer??s disease (AD) is among the most important health-care problems in the world. The two pathological hallmarks of AD are extracellular neuritic amyloid plaques and intracellular neurofibrillary tangles. The aggregation of A?? and ??-sheet formation are considered to be the critical events which render these peptides neurotoxic. AD is affecting a large percentage of the elderly around the world. Many studies have been done on drugs to cure or at least slow Alzheimer??s disease. Most drugs produced for this disease aim at compensating for the performance of specific cell groups affected by the disease or restoring the function of these cells.This study examined the interaction of crocin, the main pigment of saffron, with the amyloid-?? peptides 1?+?40 (A?? 40) to determine the effects on peptide conformation and fibril formation using fluorescence spectroscopy, CD spectroscopy and electron microscopy. ThT data demonstrated the appearance of well-defined amyloid fibrils indicating an enhanced nucleation of A??40. Incubation of pre-formed A??40 fibrils with crocin resulted in extensive lateral aggregation and precipitation of the fibrils. Consistent with this, electron microscopy data indicated that crocin decreased the number of fibrils formed and significantly reduced the average fibril length of A??40 as assessed by low levels of thioflavin T binding data. The mechanism by which, crocin prevented fibril formation was demonstrated by ANS binding assay and CD spectroscopy. In summary, crocin interacts with A?? peptides and prevents amyloid formation. This means that it has the potential to be an important therapeutic drug against AD.     

Land use–related Changes in Aboveground Carbon Stocks of Austria’s Terrestrial Ecosystems

Land-use changes considerably alter the patterns and processes of terrestrial ecosystems. In an attempt to assess the impact of the human domination of ecosystems, this study quantifies the effect of human activities on aboveground carbon stocks in vegetation, based on a comparison of potential and actual vegetation in Austria. Following an accounting approach, statistical and GIS data on vegetation, elevation, land use, biomass harvest, as well as forest inventories and real estate statistics, were entered into the assessment, which was performed at the level of municipalities (n = 2,350). The results show that aboveground carbon storage in Austria has been considerably reduced by human activities. Actual vegetation contains 64% less carbon than would be expected in potential vegetation. The conversion of forests to cropland, grasslands, and urban areas has contributed 77% to this reduction in carbon stocks, the remaining 23% is due to forest management. In Austria, aboveground carbon stocks in forests have been reduced by 30% due to reductions in stand age and changes in forest species composition. Placing the data in a historical context, this analysis suggests that the current terrestrial carbon sink is a reversal of past carbon losses.     

Adaptative Value of a PKC–PKI55 Feedback Loop of Inhibition That Prevents the Kinase’s Deregulation

A 168-bp amplification product was obtained in RT-PCR experiments using a degenerate oligonucleotide designed on a five-amino acid sequence of IN, a 7-kDa protein, previously characterized as a PKC inhibitor. It was included in the coding ORF of the 1530-bp-long IMAGE clone ID 38900 (accession numbers R51337 and R51448) that produces a translation product of 6.5 kDa. The translation of the ORF conceptual reading frame allowed the preparation of the synthetic protein PKI55, which was found to inhibit and degrade both untreated nPKC d isozymes and activated cPKC isozymes. The PKI55 gene is localized in chromosome 2q35. The Repeat Maskers output showed a 533-bp-long LTR32/ERVL segment that included the PKI55 coding sequence and a complete regulatory region. The coding sequence and the structure of PKI55 were detected in a brain cDNA of Macaca fascicularis (diverged from human lineages about 25 Myr ago). Three other human genes with over 60% identities with PKI55 were identified in three different loci (i.e., chromosomes 10, 15, and 20.) Synthesis of PKI55 was stimulated by PKC activation. A feedback loop of inhibition is established. When the PKCs are overactivated, PKI55 induces degradation of the enzyme and prevents the isozyme overexpression implicated in a number of important diseases including cancer, diabetes, and disorders of the immune system. The presence of the PKI55 sequence in Macaca fascicularis as well as in human chromosomes 10, 15, and 20 indicates a selective advantage for the PKI55 sequence and the adaptive value of the feedback mechanism. Rita Selvatici, Center of Neuroscience, University of Ferrara, Ferrara, Italy Accession Numbers: human chromosome 10 clone RP11-36N22, AL356865; human chromosome 15 clone RP11-57P19, AC009432; human chromosome 20 clone RP4-697P8, AL050403; Macaca fascicularis brain cDNA clone QnpA-21012, AB050412; cDNA clone DKFZp434H1419, AL137534; human chromosome 2q35 BAC clone RPCI11-1064L18, AC008123; IMAGE clone ID 38900, R51337 and R51448. BLAST amino acid query sequence from TBLASTN program 2.2.1 ( ).     

A consensus ethnobotany of the Q’eqchi’ Maya of Southern Belize

An ethnobotany study in collaboration with Q’eqchi’ Maya healers of Southern Belize led to a collection of 169 medicinal plant species, belonging to 67 different families. The data show the use of a majority of species from primary or secondary semi-evergreen rainforests of Southern Belize, rather than weedy species. The medicinal uses of the plants were grouped into 17 usage categories. The frequency of use for each plant and the informant consensus factor for each usage category reveals a consensus among the healers on the use of plant species as well as on the diseases treated. These results suggest a well-defined medicinal tradition.     

Covalent anthocyanin–flavonol complexes from the violet-blue flowers of Allium ‘Blue Perfume’

Three covalent anthocyanin–flavonol complexes (pigments 1–3) were extracted from the violet-blue flower of Allium ‘Blue Perfume’ with 5% acetic acid-MeOH solution, in which pigment 1 was the dominant pigment. These three pigments are based on delphinidin 3-glucoside as their deacylanthocyanin and were acylated with malonyl kaempferol 3-sophoroside-7-glucosiduronic acid or malonyl-kaempferol 3-p-coumaroyl-tetraglycoside-7-glucosiduronic acid in addition to acylation with acetic acid.By spectroscopic and chemical methods, the structures of these three pigments 1–3 were determined to be: pigment 1, (6^I-O-(delphinidin 3-O-(3^I-O-(acetyl)-β-glucopyranoside^I)))(2^VI-O-(kaempferol 3-O-(2^II-O-(3^III-O-(β-glucopyranosyl^V)-β-glucopyranosyl^III)-4^II-O-(trans-p-coumaroyl)-6^II-O-(β-glucopyranosyl^IV)-β-glucopyranoside^II)-7-O-(β-glucosiduronic acid^VI))) malonate; pigment 2, (6^I-O-(delphinidin 3-O-(3^I-O-(acetyl)-β-glucopyranoside^I)))(2^VI-O-(kaempferol 3-O-(2^II-O-β-glucopyranosyl^III)-β-glucopyranoside^II)-7-O-(β-glucosiduronic acid^VI))); and pigment 3, (6^I-O-(delphinidin 3-O-(3^I-O-(acetyl)-β-glucopyranoside^I)))(2^VI-O-(kaempferol 3-O-(2^II-O-(3^III-O-(β-glucopyranosyl^V)-β-glucopyranosyl^III)-4^II-O-(cis-p-coumaroyl)-6^II-O-(β-glucopyranosyl^IV)-β-glucopyranoside^II)-7-O-(β-glucosiduronic acid^VI))) malonate.The structure of pigment 2 was analogous to that of a covalent anthocyanin–flavonol complex isolated from Allium schoenoprasum where delphinidin was observed in place of cyanidin. The three covalent anthocyanin–flavonol complexes (pigment 1–3) had a stable violet-blue color with three characteristic absorption maxima at 540, 547 and 618 nm in pH 5–6 buffer solution. From circular dichroism measurement of pigment 1 in the pH 6.0 buffer solution, cotton effects were observed at 533 (+), 604 (−) and 638 (−) nm. Based on these results, these covalent anthocyanin–flavonol complexes were presumed to maintain a stable intramolecular association between delphinidin and kaempferol units closely related to that observed between anthocyanin and hydroxycinnamic acid residues in polyacylated anthocyanins. Additionally, an acylated kaempferol glycoside (pigment 4) was isolated from the same flower extract, and its structure was determined to be kaempferol 3-O-sophoroside-7-O-(3-O-(malonyl)-β-glucopyranosiduronic acid).     

Pattern Cladistics and the ‘Realism–Antirealism Debate’ in the Philosophy of Biology

Despite the amount of work that has been produced on the subject over the years, the ‘transformation of cladistics’ is still a misunderstood episode in the history of comparative biology. Here, I analyze two outstanding, highly contrasting historiographic accounts on the matter, under the perspective of an influential dichotomy in the philosophy of science: the opposition between Scientific Realism and Empiricism. Placing special emphasis on the notion of ‘causal grounding’ of morphological characters (sensu Olivier Rieppel) in modern developmental biology’s (mechanistic) theories, I arrive at the conclusion that a ‘new transformation of cladistics’ is philosophically plausible. This ‘reformed’ understanding of ‘pattern cladistics’ entails retaining the interpretation of cladograms as ‘schemes of synapomorphies’, but in association to construing cladogram nodes as ‘developmental-genetic taxic homologies’, instead of ‘standard Darwinian ancestors’. The reinterpretation of pattern cladistics presented here additionally proposes to take Bas Van Fraassen’s ‘constructive empiricism’ as a philosophical stance that could properly support such analysis of developmental-genetic data for systematic purposes. The latter suggestion is justified through a reappraisal of previous ideas developed by prominent pattern cladists (mainly, Colin Patterson), which concerned a scientifically efficient ‘observable/non-observable distinction’ linked to the conceptual pair ‘ontogeny and phylogeny’. Finally, I argue that a robust articulation of Antirealist alternatives in systematics may provide a rational basis for its disciplinary separation from evolutionary biology, as well as for a critical reconsideration of the proper role of certain Scientific Realist positions, currently popular in comparative biology.