Marine biological invasions in waters of the port of Novorossiysk in the Black Sea

The results of the monitoring of ballast waters of commercial vessels and research on the ecosystem biodiversity of the Novorossiysk Port are reported. Data on structure of immigrant fauna, its abundance, survival and origin of species were obtained. It has been established that the risk of introduction of Mediterranean species into the Novorossiysk Bay is the most probable. The basic “risk groups” are copepods and polychaetes. It has been hypothesized, that ship ballast water can become a primary factor of the “mediterranization” of the copepod fauna (Copepoda) in the northeast of the Black Sea. During the period of research in the Novorossiysk Bay, 36 species of Mediterranean copepods were recorded. A massive number of the cyclopoid copepod Oithona brevicornis Giesbr., 1891, a new species for the Black Sea, was recorded in samples collected in the autumn of 2005 and 2006. The status of the invader was attributed to the polychaete of the Streblospio genus. The necessity of ship ballast water control in Russia and the development of methodology, methods, and regulations for the prevention of the intrusion of pathogenic and potentially dangerous organisms by marine traffic were corroborated.     

A descriptive study of some Antarctic notaspidean opisthobranchs (Gastropoda), with description of a new genus and species

During the expedition “ANTARTIDA 9101”, organized by the Spanish Oceanographic Institute to the South Orkney Islands, four specimens of notaspidean gastropods were collected. Three of them have been identified as Bathyberthella antarctica Willan and Bertsch, 1987. However, one specimen, although externally similar to B. antarctica, had an internal anatomy exhibiting features that have enabled us to consider it to be a new genus and species. This new taxon is characterized by the presence of jaws without mandibular elements, and a vaginal gland that partially surrounds the distal region of the vaginal duct. In this paper the new genus and species is described. Additional anatomical data of the specimens of B. antarctica collected during the expedition are also included.     

Specific effects and biofeedback versus biofeedback-assisted self-regulation training

In any field, clear and logical conceptualizations are the basis of accurate models → correct research design → correct results → correct conclusions → advancement in the field. Faulty conceptualizations → faulty models → faulty research design → faulty results → faulty conclusions → confusion. In analyzing the conceptualizations of “biofeedback” as expressed by John Furedy (1987) in, “Specific versus Placebo Effects in Biofeedback Training: A Critical Lay Perspective,” we focus on two issues: Does biofeedback have a treatment effect? Is biofeedback necessary for the training effect? In discussing issue (1) we describe the multiple meanings of “biofeedback” and raise the fundamental question: Is biofeedback a treatment? We argue that faulty conceptualizations of clinical biofeedback (1) assume that the treatment in clinical biofeedback is “biofeedback” with specific effects, (2) assume that the scientific basis of biofeedback is dependent upon demonstrations of these specific effects through double-blind designs that distinguish “specific” from “placebo effects,” and (3) trivialize clinical research by attempting to determine the usefulness of biofeedback information — usefulness that is already understood logically by professionals and consumers and demonstrated by clinical studies in the laboratory and in the clinic. We further argue that accurate conceptualizations of clinical biofeedback (1) identify self-regulation skills as the treatment with specific effects of physiological change and symptom reduction, and (2) describe the use of information from biofeedback instruments as scientific verification of self-regulation skills. Finally, the scientific basis of clinical biofeedback is based on (1) evidence from experimental and clinical control studies that have demonstrated the effectiveness of self-regulation skills for symptom alleviation, and (2) the use of biofeedback instruments to verify the acquisition of self-regulatory skills, thus fulfilling the scientific dictum of verifiability.     

Blobel and Sabatini’s “Beautiful Idea”: Visual Representations of the Conception and Refinement of the Signal Hypothesis

In 1971, Günter Blobel and David Sabatini proposed a novel and quite speculative schematic model to describe how proteins might reach the proper cellular location. According to their proposal, proteins destined to be secreted from the cell contain a “signal” to direct their release. Despite the fact that Blobel and Sabatini presented their signal hypothesis as a “beautiful idea” not grounded in experimental evidence, they received criticism from other scientists who opposed such speculation. Following the publication of the 1971 model, Blobel persisted in conducting experiments and revising the model to incorporate new data. In fact, over the period of 1975–1984, Blobel and colleagues published five subsequent schematic models of the signal hypothesis, each revised based on new laboratory evidence. I propose that the original 1971 model can be viewed as an epistemic creation. Additionally, analysis of the subsequent schematic diagrams over the period of 1975–1984 allows one to track Blobel’s changing conception of an epistemic object over time. Furthermore, the entire series of schematic diagrams presented by Blobel from 1971 to 1984 allow one to visualize the initial conception and subsequent reworking of a scientific theory. In 1999, Blobel was awarded the Nobel Prize in Physiology or Medicine for his work on the signal hypothesis, which was ultimately supported by experimental evidence gathered after the speculative model was published.     

First findings of small-head eel cod Notomuraenobathys microcephalus (Muraenolepididae: Gadiformes) in the magellanean subantarctic with comments on the evolutionary history of the family

Notomuraenobathys microcephalus (Norman, 1937) was found for the first time outside the Southern Ocean. Smallhead eel cod was sampled twice in the Patagonian-Falkland region during the scientific cruises of Russian research vessels “Akademik Kurchatov” (1971) and “Professor Mesyatsev” (1974). The first sample allowed documenting the northernmost margin of the geographical range of the Muraenolepididae family in southwestern Antarctica, and the second one is extraordinary the shallowest depth (about 750 m) of inhabiting of adults specimens of this species. The scenario of early evolution stages of the divergence of muraenolepidids is suggested.     

Evolved Biofilm: Review on the Experimental Evolution Studies of Bacillus subtilis Pellicles

For several decades, laboratory evolution has served as a powerful method to manipulate microorganisms and to explore long-term dynamics in microbial populations. Next to canonical Escherichia coli planktonic cultures, experimental evolution has expanded into alternative cultivation methods and species, opening the doors to new research questions. Bacillus subtilis, the spore-forming and root-colonizing bacterium, can easily develop in the laboratory as a liquid–air interface colonizing pellicle biofilm. Here, we summarize recent findings derived from this tractable experimental model. Clonal pellicle biofilms of B. subtilis can rapidly undergo morphological and genetic diversification creating new ecological interactions, for example, exploitation by biofilm non-producers. Moreover, long-term exposure to such matrix non-producers can modulate cooperation in biofilms, leading to different phenotypic heterogeneity pattern of matrix production with larger subpopulation of “ON” cells. Alternatively, complementary variants of biofilm non-producers, each lacking a distinct matrix component, can engage in a genetic division of labor, resulting in superior biofilm productivity compared to the “generalist” wild type. Nevertheless, inter-genetic cooperation appears to be evanescent and rapidly vanquished by individual biofilm formation strategies altering the amount or the properties of the remaining matrix component. Finally, fast-evolving mobile genetic elements can unpredictably shift intra-species interactions in B. subtilis biofilms. Understanding evolution in clonal biofilm populations will facilitate future studies in complex multispecies biofilms that are more representative of nature.     

A new conception of the shoot of higher plants

According to the classical model, the “shoot” consists only of the categories “caulome” (“stem” sensu lato) and “phyllome” (“leaf” sensu lato), (and “root” in cases of “adventitious” root formation). If lateral shoots are present, their position is axillary. Consequently, caulome as well as phyllome are inserted on the caulome and only on the caulome. This classical model of the shoot has two disadvantages of great consequence: (1) Intermediate organs cannot be accepted as such, but have to be interpreted (i.e. categorized) as either caulome or phyllome (or root) by distortion of the actual similarity. (2) Certain positional changes of organs cannot be accepted as such, but have to be “explained” by congenital fusion. The new conception of the shoot will have the advantages of the classical model but not its disadvantages. Hence, the shoot may consist of the following parts: (main and lateral) shoot, caulome, phyllome, root, emergence, and structures intermediate between (i.e. partially homologous to) any of the preceding. Thus, the five categories of the classical model, namely “shoot”, “caulome”, “phyllome”, “root” and “emergence” are no longer mutually exclusive; they may merge into each other due to an actual or potential continuum. Intermediate organs are therefore accepted as such; for example, an organ may be characterized as an intermediate form between a caulome and a phyllome. Besides intermediate forms, all changes in position are accepted as such. Hence, the following positional relations are possible: caulome and phyllome may be inserted on the caulome, caulome and phyllome may be inserted on the phyllome; roots may be inserted on caulome or phyllome; intermediate forms may be inserted on the caulome, phyllome, or other intermediate forms. Consequences of the new conception for morphological research are pointed out, especially for homologization, evolutionary considerations, and the direction in which research progresses.     

Observations of the walrus (Odobenus rosmarus) in the Barents, Kara, and Laptev seas in 2010–2012

Data on walrus (Odobenus rosmarus) sightings during four scheduled cruises of the research expedition vessel Mikhail Somov in the Barents, Kara, and Laptev seas (August–November, 2010; September–October, 2011; November–December 2011; and July–October, 2012) and during an expedition on the Polyaris motor ship in August–September, 2012, are presented. The data collected support and expand the existing knowledge on the distribution and abundance of the Atlantic and Laptev walrus subspecies.     

Which aging in yeast is “true”?

Two model systems, “replicative aging” and “chronological aging” (CA), which are used for gerontological research on the yeast Saccharomyces cerevisiae, are compared. In the first case, the number of daughter cells generated by an individual mother cell before cell propagation irreversibly stops is analyzed. This makes the model very similar to the well-known Hayflick model. In the case of CA, the survival of yeast cell population in the stationary phase of growth is studied. It is noted that the second model is similar to the “stationary phase aging” model, which is used in the author’s laboratory for cytogerontological studies on animal and human cells. It is assumed that the concept of cell proliferation restriction as the main cause of age-related accumulation in the cells of multicellular organisms of macromolecular defects (primarily DNA damage) leading to deterioration of tissue and organ functioning and, as a result, to an increase in the death probability allows explaining how the aging process proceeds in almost any living organisms. Apparently, in all cases, this process is initiated by the appearance of slow propagating (or not propagating at all) cells, which leads to the termination of “dilution,” with the help of new cells, of macromolecular defects accumulating at the level of whole cell population. It is concluded that data on the geropromoter or geroprotector activity of various factors obtained in tests on the yeast CA model can be used with a high reliability to understand the mechanisms of human aging and longevity.     

Mort ou persistance du darwinisme ? Regard d’un épistémologue

The article examines why evolutionary biologists have been haunted by the question whether they are “Darwinian” or “non-Darwinian” ever since Darwin's Origin of species. Modern criticisms addressed to Darwinism are classified into two categories: those concerning Darwin's hypothesis of “descent with modification” and those addressed to the hypothesis of natural selection. In both cases, although the particular models that Darwin proposed for these two hypotheses have been significantly revised and expanded, Darwin's general framework has constrained and canalized evolutionary research, in the sense that it has settled an array of possible theoretical choices. Gould's changing attitudes regarding Darwinism is taken as a striking illustration of this interpretation.     

A simulation support system for solving large physiological models on microcomputers

Although physiological modeling and computer simulation have become useful research tools to test new scientific theories and to design and analyze laboratory experiments, developing a new model can be a tedious process because the investigator must often write very complex and specific routines for data input and output. To facilitate the design of new models (as well as the use of existing models), we have developed MODSIM, a FORTRAN-based simulation support system for the IBM PC computer than can accommodate very large dynamic models having up to several thousand equations. It provides the investigator with utilities for continuous on-line graphical and/or tubular output, as well as facilities for dynamic interaction with the model. The user must only supply a model as a list of mathematical equations written in FORTRAN, along with the initial values of the model variables and parameters. The model is precompiled, compiled, and then linked to the MODSIM utilities. Without further programming, the user can then solve the model, select variables for graphical output, and stop the model at any time to analyze the data or to change a parameter before resuming the simulation. This simulation system makes it very easy to develop new models that actively interact with the experimental research of the investigator.     

Embryonic stem cells in science and medicine,part II: Law,ethics, and the continuing need for dialogue

Just as our first article, “Embryonic Stem Cells in Science and Medicine: An Invitation for Dialogue,” in the December 2007 issue of Gender Medicine went to press, two groups of researchers had just announced that adult human somatic cells had been reprogrammed to behave like pluripotent stem cells, and that the reprogrammed cells were able to differentiate into cell types of the 3 germ layers in vitro and in a mouse model. A third group has since done so. Because the reprogrammed cells were not embryonic in origin, the announcements were heralded as “stunning” and “leaps forward,” because, it was argued, the ability to generate stem cells, without destroying embryos in the process, would avoid the difficult ethical questions raised by human embryonic stem (hES) cell research. This article addresses the most recent announcements and briefly retraces the relevant history so that we may consider whether the moral, ethical, and social issues do in fact disappear as a result of these new advancements. We conclude that, despite the hoopla, little has changed. If indeed there were ethical issues surrounding hES cell research, they remain—and remain as urgent to address and resolve as they had been previously. Lastly, we argue that the medical and scientific communities continue to do themselves a disservice by failing to create a cohesive governing body to address and make concrete recommendations concerning the moral, ethical, and related social issues affecting their communities.     

ICJ's Decision in Australia v. Japan: Giving up the Spear or Refining the Scientific Design?

The case Whaling in the Antarctic (Australia v. Japan) decided by the International Court of Justice is a landmark that introduces new parameters for measuring the “reasonableness” of scientific research by permit under the International Convention on Whaling. However, aspects of these parameters and how they may be applied in future cases remain uncertain. Because the Court's interpretation of the language “for purposes of scientific research” avoids defining scientific research, the Court's decision provides only a limited degree of clarification for States that intend to operate scientific whaling programs under Article VIII of the Convention. The Court's reasonableness test is unlikely to prevent scientific whaling. States who no longer support the dual object and purpose of the Whaling Convention may want to consider negotiating a new international instrument that would be more protective of whales and their habitat.     

The proximate/ultimate distinction in the multiple careers of Ernst Mayr

Ernst Mayr's distinction between “ultimate” and “proximate” causes is justly considered a major contribution to philosophy of biology. But how did Mayr come to this “philosophical” distinction, and what role did it play in his earlier “scientific” work? I address these issues by dividing Mayr's work into three careers or phases: 1) Mayr the naturalist/researcher, 2) Mayr the representative of and spokesman for evolutionary biology and systematics, and more recently 3) Mayr the historian and philosopher of biology. If we want to understand the role of the proximate/ultimate distinction in Mayr's more recent career as a philosopher and historian, then it helps to consider hisearlier use of the distinction, in the course of his research, and in his promotion of the professions of evolutionary biology and systematics. I believe that this approach would also shed light on some other important “philosophical” positions that Mayr has defended, including the distinction between “essentialism: and “population thinking.”     

Actividad de la micafungina contra las biopelículas de Candida

BackgroundMost recalcitrant infections are associated to colonization and microbial biofilm development. These biofilms are difficult to eliminate by the immune response mechanisms and the current antimicrobial therapy.AimTo describe the antifungal of micafungin against fungal biofilms based in the scientific and medical literature of recent years.MethodsWe have done a bibliographic retrieval using the scientific terms “micafungin”, “activity”, “biofilm”, “Candida”, “Aspergillus”, “fungi”, “mycos”*, susceptibility, in PubMed/Medline from the National Library of Medicine from 2006 to 2009.ResultsMost current antifungal agents (amphotericin B and fluconazole) and the new azole antifungals have no activity against fungal biofilms. However, micafungin and the rest of echinocandins are very active against Candida albicans, Candida dubliniensis, Candida glabrata, and Candida krusei biofilms but their activities are variable and less strong against Candida tropicalis and Candida parapsilosis biofilms. Moreover, they have not activities against the biofilms of Cryptococcus y Trichosporon.ConclusionsThe activity of micafungin against Candida biofilms gives more strength to its therapeutic indication for candidaemia and invasive candidiasis associated to catheter, prosthesis and other biomedical devices.     

Studies on mixing in horizontal rotating tubular bioreactor

A horizontal rotating tubular bioreactor (HRTB) is a combination of a “thin-layer bioreactor” and a “biodisc” reactor. Its interior is divided by O-ring shaped partition walls. Mixing properties of this new type of the bioreactor were investigated by using a temperature step method. The mixing simulations were done by Runge-Kutta-Fehlberg numerical integration. Adjustable parameters of the “spiral flow” model were optimised by Monte-Carlo method. In this investigation, the structured “spiral flow” model (containing four adjustable parameters) was tested in a wide range of experimental conditions. The results show that the structured “spiral flow” model is capable to describe the mixing in HRTB in the whole range of both bioreactor operational parameters (n and D).     

Marine scientific research under emerging ocean law

Abstract

The traditional “fifth freedom”; of the high seas—freedom of scientific research—has been considerably eroded by recent coastal state claims to 200‐mile offshore zones. Insofar as these claims include competence to regulate marine scientific research, they are about to be endorsed in the adoption of a new Law of the Sea Convention by the Third U.N. Conference on the Law of the Sea. The author assesses the significance of the claims and examines the features of the “consent regime”; established through the negotiations at the Conference.     

Life history focus on a malaria parasite: linked traits and variation among genetic clones

Life history theory has long been a major campaign in evolutionary ecology, but has typically focused only on animals and plants. Life history research on single-celled eukaryotic protists such as malaria parasites (Plasmodium) will offer new insights into the theory’s general utility as well as the parasite’s basic biology. For example, parasitologists have described the Plasmodium life cycle and cell types in exquisite detail, with little discussion of evolutionary issues such as developmental links between traits. We measured 10 life history traits of replicate single-genotype experimental Plasmodium mexicanum infections in its natural lizard host to identify groups of linked traits. These 10 traits formed 4 trait groups: “Rate/Peak” merges measures of growth rate and maximum parasitemia of infections; “Timing” combines time to patency and maximum parasitemia; “Growth Shape” describes the fit to an exponential growth curve; and “Sex Ratio” includes only the gametocyte sex ratio. Parasite genotype (clone) showed no effect on the life history trait groups, with the exception of gametocyte sex ratio. Therefore, variation in most life history traits among infections appears to be driven by environmental (individual host) effects. The findings support the model that life history traits are often linked by developmental constraints. Understanding why life history traits of Plasmodium are linked in this way would offer a new window into the evolution of the parasites, and also should inform public health efforts to control infection prevalence.     

Dwarf toad plunderfish Pogonophryne minor sp. n. (Artedidraconidae; Nototheniodei; Perciformes)—a new species and one of the smallest species of autochthonous ichthyofauna of marginal seas of the Antarctic continent

A new species Pogonophryne minor sp. n. based on materials of Antarctic expeditions on research vessels Chatyr-Dag and Ob’ to the East Antarctica is described. The type specimens of the new species were caught in the Mawson and Davis seas at depths 420–540 m. The comparison of the new species with two other species of the “marmorata” group of the genus Pogonophryne: P. platypogon Eakin, 1988 and the most closely related P. marmorata Norman, 1938 is provided.