Methods used for analyses of “environmentally” damaged nucleic acids

In this review, we present various techniques, currently applied in many laboratories, which are useful in the detection of “environmentally”-induced damage to DNA. These techniques include: (a) chromatographic methods, which allow determination of chemical changes within DNA, be they formation of adducts with or oxidation of bases in DNA; (b) electrophoretic methods, which facilitate finding the site(s) in DNA where that chemical modification occurred; and (c) immunological assays, which help to detect DNA damage using externally produced antibodies that recognize the specific chemical changes in DNA or its fragments, as well as by detection of autoantibodies that develop in response to environmental exposures of animals and humans.     

Thinking in continua: beyond the “adaptive radiation” metaphor

“Adaptive radiation” is an evocative metaphor for explosive evolutionary divergence, which for over 100 years has given a powerful heuristic to countless scientists working on all types of organisms at all phylogenetic levels. However, success has come at the price of making “adaptive radiation” so vague that it can no longer reflect the detailed results yielded by powerful new phylogeny‐based techniques that quantify continuous adaptive radiation variables such as speciation rate, phylogenetic tree shape, and morphological diversity. Attempts to shoehorn the results of these techniques into categorical “adaptive radiation: yes/no” schemes lead to reification, in which arbitrary quantitative thresholds are regarded as real. Our account of the life cycle of metaphors in science suggests that it is time to exchange the spent metaphor for new concepts that better represent the full range of diversity, disparity, and speciation rate across all of life.     

“How” and “what” matters: Sampling method affects biodiversity estimates of reef fishes

Understanding changes in biodiversity requires the implementation of monitoring programs encompassing different dimensions of biodiversity through varying sampling techniques. In this work, fish assemblages associated with the “outer” and “inner” sides of four marinas, two at the Canary Islands and two at southern Portugal, were investigated using three complementary sampling techniques: underwater visual censuses (UVCs), baited cameras (BCs), and fish traps (FTs). We firstly investigated the complementarity of these sampling methods to describe species composition. Then, we investigated differences in taxonomic (TD), phylogenetic (PD) and functional diversity (FD) between sides of the marinas according to each sampling method. Finally, we explored the applicability/reproducibility of each sampling technique to characterize fish assemblages according to these metrics of diversity. UVCs and BCs provided complementary information, in terms of the number and abundances of species, while FTs sampled a particular assemblage. Patterns of TD, PD, and FD between sides of the marinas varied depending on the sampling method. UVC was the most cost‐efficient technique, in terms of personnel hours, and it is recommended for local studies. However, for large‐scale studies, BCs are recommended, as it covers greater spatio‐temporal scales by a lower cost. Our study highlights the need to implement complementary sampling techniques to monitor ecological change, at various dimensions of biodiversity. The results presented here will be useful for optimizing future monitoring programs.     

The use of calcium alginate gels for “solids separation” and “diffusional chromatography” of biological materials

The use of calcium alginate gels for the “Solids Separation” techniques was demonstrated by entrapment of a yeast extract in calcium alginate pellets and the study of the release of alcohol dehydrogenase and NADH into a dilute calcium chloride solution. The use of calcium alginate gels for a “Diffusional Chromatography” technique was demonstrated in a model system by a fractionation of NAD and hemoglobin release following their entrapment in calcium alginate pellets. The advantages of these techniques and their potentials are discussed.     

A newly identified group of adolescents at “invisible” risk for psychopathology and suicidal behavior: findings from the SEYLE study

This study explored the prevalence of risk behaviors (excessive alcohol use, illegal drug use, heavy smoking, reduced sleep, overweight, underweight, sedentary behavior, high use of Internet/TV/videogames for reasons not related to school or work, and truancy), and their association with psychopathology and self‐destructive behaviors, in a sample of 12,395 adolescents recruited in randomly selected schools across 11 European countries. Latent class analysis identified three groups of adolescents: a low‐risk group (57.8%) including pupils with low or very low frequency of risk behaviors; a high‐risk group (13.2%) including pupils who scored high on all risk behaviors, and a third group (“invisible” risk, 29%) including pupils who were positive for high use of Internet/TV/videogames for reasons not related to school or work, sedentary behavior and reduced sleep. Pupils in the “invisible” risk group, compared with the high‐risk group, had a similar prevalence of suicidal thoughts (42.2% vs. 44%), anxiety (8% vs. 9.2%), subthreshold depression (33.2% vs. 34%) and depression (13.4% vs. 14.7%). The prevalence of suicide attempts was 5.9% in the “invisible” group, 10.1% in the high‐risk group and 1.7% in the low‐risk group. The prevalence of all risk behaviors increased with age and most of them were significantly more frequent among boys. Girls were significantly more likely to experience internalizing (emotional) psychiatric symptoms. The “invisible” group may represent an important new intervention target group for potentially reducing psychopathology and other untoward outcomes in adolescence, including suicidal behavior.     

“Laughter” and “Smile” in Barbary Macaques (Macaca sylvanus)

In an observational study on semi-free Barbary macaques it was investigated whether the phylogenetic roots of human laughter and smile can be traced back to the genus Macaca. On the basis of morphological similarity a ‘relaxed open-mouth display’ as the phylogenetic precursor of the laughter, and a ‘silent bared-teeth display’ as the possible ancestor of the smile can be distinguished in the repertory of the Barbary macaque. Behavioural sequences from focal animal protocols were analyzed in order to establish message and meaning of both displays. Relaxed open-mouth display is regularly observed in the play interactions of juveniles. It is associated with partner-directed behaviour, it is frequently answered by a relaxed open-mouth display of the receiver, and accompanied by a special vocalization. Although up to 50% of the juvenile's play partners were higher ranking than themselves voluntary participation was the rule. Most characteristically, the behaviour patterns shown by both play partners are highly symmetrical and synchronized. Silent bared-teeth display is typically accompanied by evasive or submissive body movements, and occurs primarily in dyadic interactions, mainly by the lower ranking individual. It is not an unidirectional sign of a linear dominance hierarchy, though. Silent bared-teeth display is a frequent answer to aggressive behaviour shown by the receiver. After its performance, an increase of body contact between sender and receiver was observed. Behavioural sequences of senders and receivers are complementary, but lose their asymmetry after occurrence of the display. It is concluded that these results further support Van Hooff 's (1972) view that human laughter and smile have different phylogenetic roots: while silent bared-teeth display is a signal of submission and appeasement, relaxed open-mouth display is rightly called the ‘play face’, and is an expression of fun.     

Employing participatory surveys to monitor the illegal killing of elephants across diverse land uses in Laikipia–Samburu,Kenya

Levels and trends of illegal killing of elephants are measured by the Convention on International Trade in Endangered Species (CITES) Monitoring the Illegal Killing of Elephants (MIKE) programme in sites across Africa and Asia. In the mostly unprotected Laikipia–Samburu MIKE site in northern Kenya, elephant mortality data were collected using both standard law enforcement monitoring procedures, relying on patrolling, and participatory methods involving local communities. Qualitatively, traditional patrolling techniques were more successful in protected areas whereas participatory approaches provided more information outside protected areas, where elephant were most at risk from ivory poachers. A minimum of 35% of the 389 verified carcasses during 2001–2003 were illegally killed. In this baseline study, land uses ranked from highest to lowest by the proportion of illegally killed elephants (PIKE) were community conservation areas, government trust lands, forest reserves, private ranches, settlement areas and national reserves. PIKE trends derived from traditional and participatory data sources were similar across years and indicate elephants were at greater risk in regions outside government or privately patrolled areas. We suggest that PIKE is a useful index for comparing levels and trends in illegal killing of elephants, and that carcass ratios and presence/absence of tusks are useful proxy indicators of mortality and its causes.     

Characterization of global molecular shape transitions between “open” and “closed” protein conformations

Induced-fit configurational transitions in proteins can take many forms. In cases, we find small “closures” of a loop onto the substrate. In other cases, the structural changes triggered by a ligand involve large rearrangements that affect entire domains. The nature of these transitions is normally assessed by a visual analysis or in terms of simple local geometrical parameters, such as interresidue distances, backbone dihedral angles, and relative displacements between domains. This approach is limited and rather undiscriminating. In this work, we apply recently introduced ideas from macromolecular shape analysis to characterize the global shape changes accompanying “open closed” transitions in proteins. Here, we monitor two distinct properties simultaneously: molecular size and self-entanglements. The method is applied to some proteins exhibiting pairs of structurally different conformations (adenylate kinase, hexokinase, citrate synthase, alcohol dehydrogenase, triosephosphate isomerase, thioredoxin, and aspartate amino-transferase). The conformational change associated with these proteins is classified according to an order parameter that considers various molecular shape features. The results allow one to recognize, in a nonvisual fashion, the likely occurrence of local or global structural rearrangements. In addition, the technique provides an insight into folding features that may remain invariant during the configurational transitions. © 1996 John Wiley & Sons, Inc.     

Purification of “colony-forming” cells from immature rat testis

Follicle stimulating hormone (FSH) enhances colony formation (as a result of reaggregation) by dissociated 10-day-old rat testis cells in primary culture. The purpose of this study was to examine various cytological characteristics of the FSH-responsive cells and develop techniques for their purification. The ability of testis cells to form colonies in response to FSH (5 μg/ml) was tested at various ages and was found to be maximal at 15 days of age. No colony formation occurred at ages greater than 20 days. Using colony formation as an assay for the FSH-responsive cells, techniques were developed for their purification. Colony cells were purified on a continuous bovine serum albumin (BSA) step gradient (1 ml/step). In fractions purified in this manner and subsequently cultured 24 h with FSH (5 μg/ml) 99.4% of attached cells were colony cells. Light and electron microscopy indicated that the colony cells (1) were one cell type; (2) were not germinal cells; (3) ultrastructurally resembled in situ Sertoli cell of the immature rat testis; and (4) contained a nucleolus with satellite karyosomes, structures which are characteristic of rat Sertoli cells. The mitotic index of the purified cells was 0.014% following 24 h in 10⁻⁵ M colchicine. Based on these data, it was concluded that the FSH responsive cells in culture are Sertoli cells.     

multimark: an R package for analysis of capture–recapture data consisting of multiple “noninvasive” marks

I describe an open‐source R package, multimark , for estimation of survival and abundance from capture–mark–recapture data consisting of multiple “noninvasive” marks. Noninvasive marks include natural pelt or skin patterns, scars, and genetic markers that enable individual identification in lieu of physical capture. multimark provides a means for combining and jointly analyzing encounter histories from multiple noninvasive sources that otherwise cannot be reliably matched (e.g., left‐ and right‐sided photographs of bilaterally asymmetrical individuals). The package is currently capable of fitting open population Cormack–Jolly–Seber (CJS) and closed population abundance models with up to two mark types using Bayesian Markov chain Monte Carlo (MCMC) methods. multimark can also be used for Bayesian analyses of conventional capture–recapture data consisting of a single‐mark type. Some package features include (1) general model specification using formulas already familiar to most R users, (2) ability to include temporal, behavioral, age, cohort, and individual heterogeneity effects in detection and survival probabilities, (3) improved MCMC algorithm that is computationally faster and more efficient than previously proposed methods, (4) Bayesian multimodel inference using reversible jump MCMC, and (5) data simulation capabilities for power analyses and assessing model performance. I demonstrate use of multimark using left‐ and right‐sided encounter histories for bobcats (Lynx rufus) collected from remote single‐camera stations in southern California. In this example, there is evidence of a behavioral effect (i.e., trap “happy” response) that is otherwise indiscernible using conventional single‐sided analyses. The package will be most useful to ecologists seeking stronger inferences by combining different sources of mark–recapture data that are difficult (or impossible) to reliably reconcile, particularly with the sparse datasets typical of rare or elusive species for which noninvasive sampling techniques are most commonly employed. Addressing deficiencies in currently available software, multimark also provides a user‐friendly interface for performing Bayesian multimodel inference using capture–recapture data consisting of a single conventional mark or multiple noninvasive marks.     

Phase separation and drop size distributions in “homogeneous” Na-alginate/Na-caseinate mixtures

Phase separation and drop size distributions in dilute Na-caseinate/Na-alginate mixtures has been investigated using simultaneously two different measuring techniques: light scattering and image analysis. It has been found that even at very low concentrations of either polymer, where according to literature data the mixture should be homogenous, two phases can be observed. This phase separation was detected by both techniques and in each case, the drop size distributions measured by each of them were in good agreement.     

Mighty mice: Transgenic technology “knocks out” questions of matrix metalloproteinase function

Matrix metalloproteinases (MMP) comprise a family of structurally related proteinases that are believed to play a critical role in many physiological and pathological processes. Transgenic technology offers the possibility of determining whether MMPs contribute directly to these processes. For example, gain of function and loss of function models have confirmed causative roles of MMPs in the development of pulmonary emphysema and unexpectedly uncovered an MMP. dependent mechanism of inflammatory cell recruitment. Limitations of these techniques and powerful applications on the horizon are also presented as we embark on an era where controlled experiments can be performed in complex mammalian models.     

Evolution of Protein Targeting into “Complex” Plastids: The “Secretory Transport Hypothesis”

Abstract: In algae different types of plastids are known, which vary in pigment content and ultrastructure, providing an opportunity to study their evolutionary origin. One interesting feature is the number of envelope membranes surrounding the plastids. Red algae, green algae and glaucophytes have plastids with two membranes. They are thought to originate from a primary endocytobiosis event, a process in which a prokaryotic cyanobacterium was engulfed by a eukaryotic host cell and transformed into a plastid. Several other algal groups, like euglenophytes and heterokont algae (diatoms, brown algae, etc.), have plastids with three or four surrounding membranes, respectively, probably reflecting the evolution of these organisms by so‐called secondary endocytobiosis, which is the uptake of a eukaryotic alga by a eukaryotic host cell. A prerequisite for the successful establishment of primary or secondary endocytobiosis must be the development of suitable protein targeting machineries to allow the transport of nucleus‐encoded plastid proteins across the various plastid envelope membranes. Here, we discuss the possible evolution of such protein transport systems. We propose that the secretory system of the respective host cell might have been the essential tool to establish protein transport into primary as well as into secondary plastids.     

Speciation and the “shifting balance” in a continuous population

Shifts between adaptive peaks, caused by sampling drift, are involved in both speciation and adaptation via Wright's “shifting balance.” We use techniques from statistical mechanics to calculate the rate of such transitions for a population in a single panmictic deme and for a population which is continuously distributed over one- and two-dimensional regions. This calculation applies in the limit where transitions are rare. Our results indicate that stochastic divergence is feasible despite free gene flow, provided that neighbourhood size is low enough. In two dimensions, the rate of transition depends primarily on neighbourhood size N and only weakly on selection pressure (≈s^k exp(− cN)), where k is a number determined by the local population structure, in contrast with the exponential dependence on selection pressure in one dimension (≈exp(− cN √s)) or in a single deme (≈exp(− cNs)). Our calculations agree with simulations of a single deme and a one-dimensional population.     

“Capacity”, “best interests”, “will and preferences” and the UN Convention on the Rights of Persons with Disabilities

The United Nations (UN) Convention on the Rights of Persons with Disabilities (CRPD) is the most up‐to‐date international legal instrument concerning the rights of persons with disabilities. Such persons are taken to include those with serious mental disorders. According to an authoritative interpretation of a crucial Article (Article 12 ‐ Equal recognition before the law) by the UN CRPD Committee, involuntary detention and treatment of people with mental health disabilities are prohibited under the Convention. Both conventional mental health law and “capacity‐based” law are deemed to violate the Convention. However, some other UN bodies are not in full agreement (for example, the UN Human Rights Committee and the Subcommittee on Prevention of Torture and Other Cruel, Inhuman or Degrading Treatment or Punishment), while others are less explicitly absolutist (for example, the Human Rights Council). Furthermore, strong criticisms of the position of the CRPD Committee have been mounted from a number of academic quarters. These criticisms center on whether the role of a person's ability to make a decision can be ignored, no matter the circumstances. Much of the above debate turns on the concept of “legal capacity” and the now often‐repeated precept that one must always respect the “will and preferences” of the person with a disability. However, “will and preferences” remains undefined. In this paper, I offer an analysis of “will and preferences” that can clarify interventions that may be acceptable or non‐acceptable under the terms of the UN Convention.     

Low-Resolution Density Maps from Atomic Models: How Stepping “Back” Can Be a Step “Forward”

Atomic-resolution structures have had a tremendous impact on modern biological science. Much useful information also has been gleaned by merging and correlating atomic-resolution structural details with lower-resolution (15–40 Å), three-dimensional (3D) reconstructions computed from images recorded with cryo-transmission electron microscopy (cryoTEM) procedures. One way to merge these structures involves reducing the resolution of an atomic model to a level comparable to a cryoTEM reconstruction. A low-resolution density map can be derived from an atomic-resolution structure by retrieving a set of atomic coordinates editing the coordinate file, computing structure factors from the model coordinates, and computing the inverse Fourier transform of the structure factors. This method is a useful tool for structural studies primarily in combination with 3D cryoTEM reconstructions. It has been used to assess the quality of 3D reconstructions, to determine corrections for the phase-contrast transfer function of the transmission electron microscope, to calibrate the dimensions and handedness of 3D reconstructions, to produce difference maps, to model features in macromolecules or macromolecular complexes, and to generate models to initiate model-based determination of particle orientation and origin parameters for 3D reconstruction.     

Cetacean By-Catch in the Korean Peninsula—by Chance or by Design?

Whaling remains one of the most contentious issues in global conservation. In South Korea, where commercial and subsistence whaling are both illegal, domestic sales of cetacean products such as skin, blubber and red meat are allowed if they are accidently caught. However, environmental groups have claimed that the high price of meat may be acting as an incentive for illegal hunting and ‘deliberate by-catch’ where whales are intentionally killed or left to die by fishermen when they become trapped in their nets. In this paper we investigate the issue of deliberate by-catch and illegal hunting of the protected Minke J-stock population in Korean waters using grounded theory, an approach that allows theories and understanding to emerge from the analysis of both qualitative and quantitative data. Our research suggests that deliberate by-catch is almost certainly taking place but that illegal hunting and/or illegal importation from Japan may be far more significant sources of Minke whale meat. We discuss possible measures to reduce incentives for deliberate by-catch and illegal hunting such as the introduction of mandatory reporting of quantities supplied and consumed in restaurants and a tax on meat sales at auction. More generally, our research illustrates how the analysis of price movements can shed light on the scale of illegal wildlife trade and how a combination of both qualitative and quantitative methodologies can provide understanding of a complex, multifaceted conservation issue.     

Molecular dynamics simulations of a winter flounder “antifreeze” polypeptide in aqueous solution

A winter flounder antifreeze polypeptide (HPLC-6) has been studied in vacuo and in aqueous solution using molecular dynamics computer simulation techniques. The helical conformation of this polypeptide was found to be stable both in vacuum and in solution. The major stabilizing interactions were found to be the main-chain hydrogen bonds, a salt-bridge interaction, and solute–solvent hydrogen bonds. A significant bending in the middle of the polypeptide chain was observed both in vacuo and in solvent at 300 K. Possible causes of the bending are discussed. From simulations of mutant polypeptide molecules in vacuo, it is concluded that the bend in the native polypeptide was caused by side chain to backbone hydrogen bond competition involving the Thr 24 side chain and facilitated by strains on the helix resulting from the Lys 18-Glu 22 salt bridge. © 1993 John Wiley & Sons, Inc.     

Remotely-sensed indicators for monitoring the general condition of “natural habitat” in watersheds: an application for Delaware’s Nanticoke River watershed

Over the past two decades there has been increasing interest in developing indicators to monitor environmental change. Remote sensing techniques have been primarily used to generate information on land use/land cover changes. The US Fish and Wildlife Service has used this technology to monitor wetland trends and recently developed a set of remotely-sensed indicators to characterize and assess trends in the integrity of natural habitat in watersheds. The indices largely focus on the extent of “natural” cover throughout a given watershed, with an emphasis on locations important to fish, wildlife, and water quality. Six indices address natural habitat extent and four deal with human-caused disturbance. A composite index of natural habitat integrity combining the habitat extent and habitat disturbance indices may be formulated to provide an overall numeric value for a watershed or subbasin. These indices facilitate comparison between watersheds (and subbasins) and assesssment of trends useful for environmental monitoring. This paper describes the indices and presents an example of their application for characterizing and assessing conditions of subbasins within Delaware’s Nanticoke River watershed.     

Genomic analyses of a “living fossil”: The endangered dove‐tree

Davidia involucrata Baill, also known as the dove‐tree, is a living fossil and an endangered species currently restricted to the mountains of southwestern and central China. It has a beautiful and innovative trait of high horticultural value: two white bracts covering the flower caputila. Here, we report on the chromosome‐scale genome of this species using single‐molecule real‐time long reads and chromosome conformation capture (Hi‐C) techniques. This species has a larger genome size of 1,169 Mb and contains relatively more genes (42,554) than the closely related species Camptotheca acuminata (397 Mb and 31,825 genes). Both species shared one recent whole genome duplication before their divergence. The expansion of the repetitive elements after their divergence contributed greatly to the increase in the genome size of the dove‐tree. Photosynthesis‐related genes were almost absent or showed reduced expression in the bracts of the dove‐tree, while defence‐ and chemical‐related genes increased greatly, highlighting the important roles of the bracts in protecting flowers and attracting pollinators. The effective population size of the dove‐tree continuously decreased during the climate changes of the Quaternary. Such climate sensitivity should be fully considered in conservation efforts for this relict endangered species in the context of continuous climate warming in the future.