Source-sink landscape theory and its ecological significance

Exploring the relationships between landscape pattern and ecological processes is the key topic of landscape ecology, for which, a large number of indices as well as landscape pattern analysis model were developed. However, one problem faced by landscape ecologists is that it is hard to link the landscape indices with a specific ecological process. Linking landscape pattern and ecological processes has become a challenge for landscape ecologists. “Source” and “sink” are common concepts used in air pollution research, by which the movement direction and pattern of different pollutants in air can be clearly identified. In fact, for any ecological process, the research can be considered as a balance between the source and the sink in space. Thus, the concepts of “source” and “sink” could be implemented to the research of landscape pattern and ecological processes. In this paper, a theory of sourcesink landscape was proposed, which include: (1) In the research of landscape pattern and ecological process, all landscape types can be divided into two groups, “source” landscape and “sink” landscape. “Source” landscape contributes positively to the ecological process, while “sink” landscape is unhelpful to the ecological process. (2) Both landscapes are recognized with regard to the specific ecological process. “Source” landscape in a target ecological process may change into a “sink” landscape as in another ecological process. Therefore, the ecological process should be determined before “source” or “sink” landscape were defined. (3) The key point to distinguish “source” landscape from “sink” landscape is to quantify the effect of landscape on ecological process. The positive effect is made by “source” landscape, and the negative effect by “sink” landscape. (4) For the same ecological process, the contribution of “source” landscapes may vary, and it is the same to the “sink” landscapes. It is required to determine the weight of each landscape type on ecological processes. (5) The sourcesink principle can be applied to non-point source pollution control, biologic diversity protection, urban heat island effect mitigation, etc. However, the landscape evaluation models need to be calibrated respectively, because different ecological processes correspond with different source-sink landscapes and evaluation models for the different study areas. This theory is helpful to further study landscape pattern and ecological process, and offers a basis for new landscape index design. __________ Translated from Acta Ecologica Sinica, 2006, 26(5): 1444–1449 [译自: 生态学报]     

History of the use of “cedar glades” and other descriptive terms for vegetation on rocky limestone soils in the Central Basin of Tennessee

Use of “cedar glades” and other terms by geologists, botanists, soil scientists, and zoologists to describe vegetation on rocky limestone soils in the Central (Nashville) Basin of Tennessee from 1851 to 2003 is reviewed. Historically, in the Central Basin “cedar glades” has been applied to the rocky openings / redcedar / redcedar-hardwood / hardwood forest complex primarily on the (thin-bedded) Lebanon limestone but also on other (thick-bedded) Ordovician limestones. However, “cedar glades,” “limestone glades,” and “limestone cedar glades” increasingly are being used by botanists and plant ecologists for the rocky openings only, which have C4 native annual grass-C3 annual/perennial forb-cryptogam-dominated vegetation. Some erroneous statements in the literature that have resulted from misinterpretation or misunderstanding of “cedar glades” and other terms are discussed. Finally, a graphical model of the (apparent) pathways of development of cedar glade vegetation from bare rock to forest in the Central Basin is presented.     

Inventory, differentiation, and proportional diversity: a consistent terminology for quantifying species diversity

Almost half a century after Whittaker (Ecol Monogr 30:279–338, 1960) proposed his influential diversity concept, it is time for a critical reappraisal. Although the terms alpha, beta and gamma diversity introduced by Whittaker have become general textbook knowledge, the concept suffers from several drawbacks. First, alpha and gamma diversity share the same characteristics and are differentiated only by the scale at which they are applied. However, as scale is relative––depending on the organism(s) or ecosystems investigated––this is not a meaningful ecological criterion. Alpha and gamma diversity can instead be grouped together under the term “inventory diversity.” Out of the three levels proposed by Whittaker, beta diversity is the one which receives the most contradictory comments regarding its usefulness (“key concept” vs. “abstruse concept”). Obviously beta diversity means different things to different people. Apart from the large variety of methods used to investigate it, the main reason for this may be different underlying data characteristics. A literature review reveals that the multitude of measures used to assess beta diversity can be sorted into two conceptually different groups. The first group directly takes species distinction into account and compares the similarity of sites (similarity indices, slope of the distance decay relationship, length of the ordination axis, and sum of squares of a species matrix). The second group relates species richness (or other summary diversity measures) of two (or more) different scales to each other (additive and multiplicative partitioning). Due to that important distinction, we suggest that beta diversity should be split into two levels, “differentiation diversity” (first group) and “proportional diversity” (second group). Thus, we propose to use the terms “inventory diversity” for within-sample diversity, “differentiation diversity” for compositional similarity between samples, and “proportional diversity” for the comparison of inventory diversity across spatial and temporal scales. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Typostrophism in Palaeozoic Ammonoids?

The anti-Darwinian “Typostrophe Theory” of O.H.Schindewolf can be put to the test by revisiting the ammonoid examples on which this macroevolutionary model was founded. It is shown that none of the three theoretical elements saltationism, internalism, and cyclism can be supported by empirical data obtained from ammonoid research. Putative saltations (“Typogenesis”) were feigned because of the lack of knowledge of intermediate forms. Internalistic and orthogenetic development (“Typostasis”) can only be favoured by neglecting possible functions of morphological characters. Preprogrammed extinction of “degenerated” clades (“Typolysis”) is unlikely when ruling out anthropocentric views regarding ammonoid morphology. In terms of evolution of Palaeozoic ammonoids, there is no basis for the preference of the “Typostrophe Theory” or some of its composing elements, including the “Type Concept” and “Proterogenesis”, over the Darwinian evolutionary model and the Modern Synthesis.      

Electrocardiographic image of myocardial ischemia: Real measurements and biophysical models

The peculiarities of the genesis of electrocardiosignal under myocardial ischemia in connection with an increase of its electrical inhomogeneity, as well as the electrophysiological mechanisms of morphological changes of the T wave of the electrocardiogram, including its “symmetrization” have been considered. A systemic approach to the problem has been used, which combines the mathematical, computer, and physiological modeling of the cardiac electrical activity with studies of the electric field of the human heart in terms of biophysical models. A database for the repolarization parameters of experimental electrocardiosignals (“Norm” and “Ischemia” samples) has been formed. The parameters of the ST-T interval and T wave, which could characterize the symmetry of the latter, and some additional properties of the repolarization process have been obtained. The methods of mathematical modeling were used also. Computer experiments were carried out on a system for 3D modeling of the cardiac electrical activity at different structural levels of the object. By the results of preliminary analysis, the β _T index, which is calculated as the ratio of two maximum absolute values of the derivative of the cardiosignal at the left and right of the T wave apex, has been chosen as one of the main diagnostic markers of ischemia. There is reason to believe that the use of the β _T index allows one to recognize those deviations from the norm that are usually hidden from a physician in traditional ECG analysis. The ratios of repolarization intervals inside of the generalized QT interval have also appeared potentially informative. With the purpose to test and correct the hypotheses for conducting further investigations, some preliminary experiments on a low-resolution model for several alternatives of the degree, localization, and extensiveness of ischemia have been carried out. The results obtained at the first stage of the team-work are essential to the understanding of mechanisms of the genesis of an electrocardiographic image for myocardial ischemia and of interest for the biophysically sound development of new algorithms for computer cardiodiagnostics.     

Process Control as Ecosystem Management: Using the History of Sewage Treatment Plants to Analyze Ecosystem Management Practices

Industrial ecosystems are fruitful sites for examining ecosystem management. Sewage treatment plants, breweries, biotechnology reactors, and ethanol production plants are all ecosystems—complex biophysical systems in which communities of bacteria, yeast, fungi, and other organisms are maintained to extract services or resources. The industrial analog to ecosystem management is “process control”, where the industrial operator is the ecosystem manager. Process control is the management of a production process through the careful measurement and adjustment of its physical and chemical conditions. By analyzing the history of process control in activated sludge sewage treatment plants, I show the importance of craft knowledge in ecosystem management. Sewage treatment plant workers, through their experience in operating the plants, developed means of evaluating process conditions based on sight and smell rather than laboratory analysis. These craft techniques developed and persisted in spite of concerted efforts on the part of sanitary scientists to institute “scientific” control of the process based on laboratory analysis and models of microbial kinetics, suggesting that craft knowledge of ecosystem function can contribute to successful management. The craft knowledge of sewage plant workers is a kind of adaptive management, in which workers constantly adjust ecosystem parameters and observe the results. This approach is contrasted to “command and control” approaches to treatment plant automation, which have met with uneven success.     

The discovery of state transitions in photosynthesis 40 years ago

In the late 1960s, I identified an aspect of the kinetics of chlorophyll fluorescence in algal cells that I was unable to explain in terms of photochemical quenching. I proposed a novel regulatory mechanism for the distribution of light energy to photosystems I and II, which is now known by the term of “state transitions.” I also examined the “cation-dependent redistribution of light energy” to photosystems I and II and the “energy-dependent quenching” of chlorophyll fluorescence. At that time, financial constraints prevented me from measuring the emission and action spectra of chlorophyll fluorescence at liquid-nitrogen temperature and the light quality-dependent changes in the yield of chlorophyll fluorescence at room temperature. The financial problems were solved by constructing several pieces of electronic equipment using skills obtained by repairing radios when I was a high-school and college student.     

“Not <Emphasis Type="Italic">Here</Emphasis>”: Making the Spaces and Subjects of “Global Health” in Botswana

This essay argues that what makes “global health” “global” has more to do with configurations of space and time, and the claims to expertise and moral stances these configurations make possible, than with the geographical distribution of medical experts or the universal, if also uneven, distribution of threats to health. Drawing on a study of public–private partnerships supporting Botswana’s HIV/AIDS treatment program, this essay demonstrates ethnographically the processes by which “global health” and its quintessential spaces, namely “resource-limited” or “resource-poor settings,” are constituted, reinforced, and contested in the context of medical education and medical practice in Botswana’s largest hospital. Using Silverstein’s work on orders of indexicality, I argue that the terms of “global health” are best understood as chronotopic, and demonstrate how actors orient themselves and others spatio-temporally, morally, and professionally by using or refuting those terms. I conclude by arguing that taking “global health” on its own terms obscures the powerful forces by which it becomes intelligible. At stake are the frames within which medical anthropologists understand their objects of study, as well as the potential for the spaces of “global health” intervention to expand ever outward as American medical personnel attempt to calibrate their experiences to their expectations.     

The Jackprot Simulation Couples Mutation Rate with Natural Selection to Illustrate How Protein Evolution Is Not Random

Protein evolution is not a random process. Views which attribute randomness to molecular change, deleterious nature to single-gene mutations, insufficient geological time, or population size for molecular improvements to occur, or invoke “design creationism” to account for complexity in molecular structures and biological processes, are unfounded. Scientific evidence suggests that natural selection tinkers with molecular improvements by retaining adaptive peptide sequence. We used slot-machine probabilities and ion channels to show biological directionality on molecular change. Because ion channels reside in the lipid bilayer of cell membranes, their residue location must be in balance with the membrane’s hydrophobic/philic nature; a selective “pore” for ion passage is located within the hydrophobic region. We contrasted the random generation of DNA sequence for KcsA, a bacterial two-transmembrane-domain (2TM) potassium channel, from Streptomyces lividans, with an under-selection scenario, the “jackprot,” which predicted much faster evolution than by chance. We wrote a computer program in JAVA APPLET version 1.0 and designed an online interface, The Jackprot Simulation , to model a numerical interaction between mutation rate and natural selection during a scenario of polypeptide evolution. Winning the “jackprot,” or highest-fitness complete-peptide sequence, required cumulative smaller “wins” (rewarded by selection) at the first, second, and third positions in each of the 161 KcsA codons (“jackdons” that led to “jackacids” that led to the “jackprot”). The “jackprot” is a didactic tool to demonstrate how mutation rate coupled with natural selection suffices to explain the evolution of specialized proteins, such as the complex six-transmembrane (6TM) domain potassium, sodium, or calcium channels. Ancestral DNA sequences coding for 2TM-like proteins underwent nucleotide “edition” and gene duplications to generate the 6TMs. Ion channels are essential to the physiology of neurons, ganglia, and brains, and were crucial to the evolutionary advent of consciousness. The Jackprot Simulation illustrates in a computer model that evolution is not and cannot be a random process as conceived by design creationists.     

Modeling of the actomyosin ATPase activity

In the rapid “quench” kientics of myosin, the “initial phosphate burst” is the excess inorganic phosphate that is produced during the early time-course of ATP hydrolysis by myosin subfragment-1 (S-1) or HMM. In general, the existence of a Pi burst implies a rapid (i.e., generally an order of magnitude faster than the steady-state hydrolysis rate) lysis of the phospho-anhydride bond within the ATP molecule, followed by one or more slower steps that are rate limiting for the process. Thus, the presence of a Pi burst can provide an important clue to the mechanism of the reaction. However, in the case of actomyosin, this clue as long been the subject of controversy and misunderstanding. To measure the (initial) Pi burst, myosin S-1 (or HMM) is rapidly mixed with ATP and then the mixture is acid quenched after a specific time period. The medium produced contains free Pi generated from hydrolysis of the ATP. The quantitative measure of the phosphate generated in this way has always been significantly greater than that expected by steady-state “release” of Pi alone, and it is that very difference between this measured Pi after the quench and that amount of Pi expected to be released by steady-state considerations in that same time period that has been referred to as the “initial Pi burst”. Recent investigations of the kinetics of Pi release have used an entirely new method that directly measures the release of Pi from the enzyme-product complex. These studies have made reference to the properties of the “initial Pi burst” in the presence of actin, as well as to a new kinetic entity: the “burst of Pi release”, and have been often vague concerning the true nature of the initial Pi burst, as well as the properties of Pi release as predicted by the current models of the actin activation of the myosin ATPase activity. The purpose of the current article is to correct this oversight, to discuss the “burst” in some detail, and to display the kinetics predicted by the current models for the actin activation of myosin. Furthermore, predictions for the kinetics of the new “burst of Pi release” are discussed in terms of its ability to discriminate between the two current competing models for actin activation of the myosin ATPase activity.     

Decline in energy storage in the Antarctic minke whale (<Emphasis Type="Italic">Balaenoptera bonaerensis</Emphasis>) in the Southern Ocean

The annual trend in energy storage in the Antarctic minke whale was examined using catch data from all 18 survey years in the Japanese Whale Research Program (JARPA). Regression analyses clearly showed that blubber thickness, girth and fat weight have been decreasing for nearly 2 decades. The decrease per year is estimated at approximately 0.02 cm for mid-lateral blubber thickness and 17 kg for fat weight, corresponding to 9% for both measurements over the 18-year period. Furthermore, “date”, “extent of diatom adhesion”, “sex”, “body length”, “fetus length”, “latitude”, “age” and “longitude” were all identified as partially independent predictors of blubber thickness. The direct interpretation of this substantial decline in energy storage in terms of food availability is difficult, since no long-term krill abundance series is available. However, an increase in the abundance of krill feeders other than minke whales and a resulting decrease in the krill population must be considered as a likely explanation.     

The “Wild” or “Feral” Distraction: Effects of Cultural Understandings on Management Controversy Over Free-Ranging Horses (<Emphasis Type="Italic">Equus ferus caballus</Emphasis>)

Use of the terms “wild” and “feral” characterizes ongoing debate over management of free-ranging horses. However, the focus on terminology tends to obscure complex differences in meanings and cultural perception. Examining a case study in the Chilcotin region of British Columbia, we explore how the terms “wild” and “feral” distract from the underlying issues at stake in management of horses and the landscape: different ways of valuing, understanding, and relating to land and animals. To be effective in the long term, and to avoid an unwitting continuation of outdated culturally biased land management practices, future decisions regarding management of lands and free-roaming horses in the Chilcotin would benefit from an integrated process informed by both ecological and socio-cultural information.     

Closed-loop and open-loop control of posture and movement during human trunk bending

Closed-loop (CL) and open-loop (OL) types of motor control during human forward upper trunk bending are investigated. A two-joint (hip and ankle) biomechanical model of the human body is used. The analysis is performed in terms of the movements along eigenvectors of the motion equation (“eigenmovements” or “natural synergies”). Two analyzed natural synergies are called “H-synergy” (Hip) and “A-synergy” (Ankle) according to the dominant joint in each of these synergies. Parameters of CL control were estimated using a sudden support platform displacement applied during the movement execution. The CL gain in the H-synergy increased and in the A-synergy decreased during the movement as compared with the quiet standing. The analysis of the time course of OL control signal suggests that the H-synergy (responsible for the prime movement, i.e. bending per se) is controlled according to the EP theory whereas for the associated A-synergy (responsible for posture adjustment, i.e. equilibrium maintenance) muscle forces and gravity forces are balanced for any its final amplitude and therefore the EP theory is not applicable to its control.     

The roles of body size and phylogeny in fast and slow life histories

Species’ life histories are often classified on a continuum from “fast” to “slow”, yet there is no consistently used definition of this continuum. For example, some researchers include body mass as one of the traits defining the continuum, others factor it out by analysing body-mass residuals, a third group performs both of these analyses and uses the terms “fast” and “slow” in both ways, while still others do not mention body mass at all. Our analysis of European and North American freshwater fish, mammals, and birds (N = 2,288 species) shows the fundamental differences between life-history patterns of raw data and of body-mass residuals. Specifically, in fish and mammals, the number of traits defining the continuum decreases if body-mass residuals are analysed. In birds, the continuum is defined by a different set of traits if body mass is factored out. Our study also exposes important dissimilarities among the three taxonomic groups analysed. For example, while mammals and birds with a “slow” life history have a low fecundity, the opposite is true for fish. We conclude that our understanding of life histories will improve if differences between patterns of raw data and of body-mass residuals are acknowledged, as well as differences among taxonomic groups, instead of using the “fast–slow continuum” too indiscriminately for any covarying traits that appear to suit the idea.     

Is there a Real Nexus Between Ethics and Aesthetics?

Aesthetics is a vexed topic in philosophy, with a long history. For my purposes, an aesthetic experience is a foundational affective response to an object, to which terms such as “ugly”, “beautiful”, “pretty” or “harmonious” are applied. These terms are derived from a Discourse of aesthetics; some remain constant, others change from generation to generation. Aesthetics and ethics have been linked in Western thought since the days of Plato and Aristotle. This essay examines what is happening to that link in contemporary experience. It emphasises the ways in which the popular media exploit aesthetic appeal to penetrate their market, and to exploit and frame intuitive responses to current and past events. Production values, the artfulness of editors and the financial interests of producers and directors thus do much to determine contemporary aesthetic and ethical judgements. That which is beautifully presented invites the ethical involvement of the audience. Events whose images are beautifully presented constitute “hyperevidence”, a pre-judged, reinforced and amplified illusion of reality and participation. Understanding how aesthetic excellence draws audiences into ethical relationship with what is presented becomes an important part of education in ethics, including bioethics.     

Inheritance of resistance to Plum pox virus in apricot (Prunus armeniaca L.)

The inheritance of resistance to Plum pox virus (PPV) has been studied in 1,178 apricot hybrids. Seven hundred and eighteen F1 hybrids, obtained from controlled crosses between the susceptible Greek cultivar “Bebecou” and the resistant PPV cultivars of American origin (“Stark Early Orange,” ‘NJA2,” ‘Veecot,” “Sunglo,” “Harlayne,” and “Orangered”) were evaluated for resistance to the PPV-M (Marcus) strain, 8 years after artificial inoculation. The inheritance of resistance to PPV has been additionally studied for the first time in a BC₁ population of 95 apricot hybrids for four vegetative periods. Reaction of each hybrid to PPV-M was scored through visual symptoms, indexing onto GF-305 and double-antibody sandwich enzyme-linked immunosorbent assay tests. Segregation within the hybrids, determined by Chi-squared analysis, fits a 1:1 ratio (P ≤ 0.05) of the resistant vs susceptible, indicating that resistance to PPV is controlled by a single dominant gene locus and that the above six resistant cultivars are heterozygous for the trait. Plants carrying this gene may initially develop disease symptoms on leaves but eventually recover and no virus can be detected in leaves. Susceptible plants show similar symptoms initially but remain symptomatic. Inheritance of resistance to PPV also has been studied in 365 F1 hybrids by crossing the resistant cultivar “Stella” with the susceptible “Bebecou” and the resistant cultivars “Sunglo” and “NJA2,” for 8 years after inoculation. The segregation ratio was 1:0 (resistant/susceptible) suggesting that “Stella” is homozygous for the resistance trait. The purpose of this work was the enhancement of the knowledge of inheritance of resistance to PPV for the selection of new cultivars.     

Md-ACS1 and Md-ACO1 genotyping of apple (<Emphasis Type="Italic">Malus</Emphasis> x <Emphasis Type="Italic">domestica</Emphasis> Borkh.) breeding parents and suitability for marker-assisted selection

Fruit ethylene production genotypes for Md-ACS1 and Md-ACO1 were determined for 60 apple cultivars and 35 advanced breeding selections. Two alleles for each gene are commonly found in cultivated apple. Earlier studies showed that genotypes homozygous for the ACS1-2 allele produce less ethylene and have firmer fruit than ACS1-1/2 and ACS1-1/1 genotypes. ACO1 plays a minor role compared to ACS1, with homozygous ACO1-1 having lower ethylene production. In this study, ACS1-2 and ACO1-1 homozygotes had firmer fruit at harvest and after 60 days of 0–1°C cold storage compared to other genotypes. These genotypes, ACS1-2/2 and ACO1-1/1, were observed for the following 8 of 95 cultivars/selections: “Delblush”, “Fuji”, “Pacific Beauty”, “Sabina” and four breeding selections. Cultivars/selections that were homozygous ACS1-2 but not ACO1-1 were: “Ambrosia”, “Aurora Golden Gala”, “CrimsonCrisp”, “Gala”, “GoldRush”, “Huaguan”, “Pacific Rose, “Pacific Queen”, “Pinova”, “Sansa”, “Sonja”, “Sundance”, “Zestar”, and 17 breeding selections. Cultivars with the heterozygous ACS1-1/2 genotype were “Arlet”, “Braeburn”, “Cameo”, “Delicious”, “Delorgue”, “Empire”, “Enterprise”, “Ginger Gold”, “Golden Delicious”, “Granny Smith”, “Honeycrisp”, “Orin”, “Pink Lady”, “Silken”, “Suncrisp”, “Sundowner”, “Sunrise” and 11 breeding selections. No cultivars were detected homozygous for both ACS1-1 and ACO1-1, or for both ACS1-2 and ACO1-2. This study is the first large-scale allelic genotyping of both ethylene synthesis genes for a comprehensive set of apple breeding parents used in an ongoing breeding project. The data reported here are important for informative selection of parent combinations and marker-assisted selection of progeny for breeding low ethylene-producing apple cultivars for better storability and improved consumer acceptance.     

Formation and participation of nano-amyloids in pathogenesis of Alzheimer’s disease and other amyloidogenic diseases

Studies of neurodegenerative disorders attract much attention of the world scientific community due to increasing dissemination of Alzheimer’s disease. The reason for such pathologies consists in transition of a “healthy” molecule or peptide from its native conformation into a very stable “pathological” form. During this process, molecules existing in the “pathological” conformation aggregate and form amyloid fibrils that can undergo an uncontrolled increase. Novel knowledge is required on sporadic forms of Alzheimer’s disease, on the nature of triggering mechanisms of the conformational transitions of beta-amyloid fragments from normally functioning proteins into new structure, nano-beta-amyloids, that escape of neuronal and whole-body control resulted in the loss of neurons. This review summarized results of studies on the formation of amyloid fibrils and their role in pathogenesis of amyloid diseases.