The J gene of ?X174: Isolation and characterization of a J gene mutant

Summary The J gene protein of bacteriophage X174 is a component of the mature phage. The previous lack of J gene mutants has prevented an in vivo analysis of J protein functions. A X174 mutant was constructed by inserting an 11 nucleotide sequence into the J gene. This mutant, designated insJ, was viable only in the presence of a wild-type J gene carried on a plasmid that could provide J protein. An analysis of DNA synthesis during insJ mutant infection under non-permissive conditions confirmed that the J protein is not required for viral DNA synthesis.     

Chirality-induced budding: a raft-mediated mechanism for endocytosis and morphology of caveolae?

The formation of transport carriers (spherical vesicles and tubules) involves membrane budding, growth, and ultimately fission. We propose a mechanism of membrane budding, wherein the tilt and chirality of constituent molecules, confined to a patch of area A, induces buds of approximately 50-100 nm that are comparable to vesicles involved in endocytosis. Because such chiral and tilted lipid molecules are likely to exist in "rafts", we suggest the involvement of this mechanism in generating membrane buds in the clathrin and dynamin-independent, raft-component mediated endocytosis of glycosylphosphatidylinositol-anchored proteins. We argue that caveolae, permanent cell surface structures with characteristic morphology and enriched in raft constituents, are also likely to be formed by this mechanism. Thus, molecular chirality and tilt, and its expression over large spatial scales may be a common organizing principle in membrane budding of transport carriers.     

Chemistry of Cirsium and Carduus: a role in ecological risk assessment for biological control of weeds?

Prediction of host plant range and ecological impact of exotic phytophagous insects, such as insects for classical biological control of weeds, represents a major challenge. Recently, the flowerhead weevil (Rhinocyllus conicus Fröl.), introduced from Europe into North America to control exotic thistles (Carduus spp.), has become invasive. It feeds heavily on some, but not all species of native North American thistles (Cirsium spp.). We hypothesized that such non-target use among native plants could be better predicted by knowledge of characteristic chemical profiles of secondary compounds to supplement the results of host specificity testing. To evaluate this hypothesis, we reviewed the literature on the chemistry of Cirsium and Carduus thistles. We asked what compounds are known to be present, what is known about their biological activity, and whether such information on chemical profiles would have better predicted realized host range and ecological effects of R. conicus in North America. We found an extensive, but incomplete literature on the chemistry of true thistles. Two main patterns emerged. First, consistent chemical similarities and interesting differences occur among species of thistles. Second, variation occurs in biologically active groups of characteristic compounds, specifically flavonoids, sterols, alkaloids and phenolic acids, that are known to influence host plant acceptance, selection, and feeding by phytophagous insects. Surprisingly, sesquiterpene lactones, which are characterisitic in closely related Asteraceae, have not been extensively reported for Cirsium or Carduus. The minimal evidence on sesquiterpene lactones may reflect extraction methods vs. true absence. In summary, our review suggests further research on thistle chemistry in insect feeding is warranted. Also, since the exotic Canada thistle (Cirsium arvense) is an invasive thistle of current concern in North America, such research on mechanisms underlying host range expansion by exotic insects would be useful.     

Beyond the benchtop and the benthos: Dataset management planning and design for time series of ocean carbonate chemistry associated with Durafet®-based pH sensors

To better understand the impact of ocean acidification on marine ecosystems, an important ongoing research priority for marine scientists is to characterize present-day pH variability. Following recent technological advances, autonomous pH sensor deployments in shallow coastal marine environments have revealed that pH dynamics in coastal oceans are more variable in space and time than the discrete, open-ocean measurements that are used for ocean acidification projections. Data from these types of deployments will benefit the research community by facilitating the improved design of ocean acidification studies as well as the identification or evaluation of natural and human-influenced pH variability. Importantly, the collection of ecologically relevant pH data and a cohesive, user-friendly integration of results across sites and regions requires (1) effective sensor operation to ensure high-quality pH data collection and (2) efficient data management for accessibility and broad reuse by the marine science community. Here, we review the best practices for deployment, calibration, and data processing and quality control, using our experience with Durafet®-based pH sensors as a model. Next, we describe information management practices for streamlining preservation and distribution of data and for cataloging different types of pH sensor data, developed in collaboration with two U.S. Long Term Ecological Research (LTER) sites. Finally, we assess sensor performance and data recovery from 73 SeaFET deployments in the Santa Barbara Channel using our quality control guidelines and data management tools, and offer recommendations for improved data yields. Our experience provides a template for other groups contemplating using SeaFET technology as well as general steps that may be helpful for the design of data management for other complex sensors.     

A survey of osteoderm histology and ornamentation among Crocodylomorpha: A new proxy to infer lifestyle?

Osteoderms of eight extant and extinct species of crocodylomorphs are studied histologically and morphologically. Most osteoderms display the typical “crocodilian” structure with a woven-fibered matrix surrounded by an upper and a lower parallel fibered matrix. The dorsal ornamentation of those specimens consists of a pit-and-ridge structure, with corresponding remodeling mechanisms. However, an osteoderm of Iberosuchus, studied here for the first time, differs in being nearly devoid of ornamentation; moreover, it shows strong bundles of straight Sharpey's fibers perpendicular to the surface in its lateral and dorsal walls, along with a rough plywood-like structure in its basal plate. This suggests that this osteoderm was more deeply anchored within the dermis than the other osteoderms studied hitherto. This peculiar structure might have been linked to a terrestrial ecology and a specific thermoregulation strategy. Some other notosuchians in our sample do not exhibit ornamentation on their osteoderms, as opposed to neosuchians. Considering current interpretations of osteoderm function(s) in crocodilians, our observations are discussed in reference to possible ecophysiological peculiarities of Notosuchia in general, and Iberosuchus in particular.     

Chemokines: a new class of neuromodulator?

Chemokines are not only found in the immune system or expressed in inflammatory conditions: they are constitutively present in the brain in both glial cells and neurons. Recently, the possibility has been raised that they might act as neurotransmitters or neuromodulators. Although the evidence is incomplete, emerging data show that chemokines have several of the characteristics that define neurotransmitters. Moreover, their physiological actions resemble those of neuromodulators in the sense that chemokines usually have few effects by themselves in basal conditions, but modify the induced release of neurotransmitters or neuropeptides. These findings, together with the pharmacological development of agonists and antagonists that are selective for chemokine receptors and can cross the blood-brain barrier, open a new era of research in neuroscience.     

SUVi and BACH1: a new subfamily of mammalian helicases?

The RecQ family of DNA helicases have been shown to be important for the maintenance of genomic integrity in prokaryotes and eukaryotes. Members of this family are genes responsible for cancer predisposition disorders like Bloom's syndrome, Werner's syndrome and Rothmund-Thomson syndrome. Here, we show the sequence homologies between two recently identified mammalian helicases, namely SUVi and BACH1. These two genes also share strong homologies with other members of the RecQ family. On the basis of published data and sequence analysis we suggest that SUVi/BACH1 may represent a novel subfamily of mammalian helicases, functioning in the processing of lesions induced by different genotoxic agents.     

Comparative study (AFLP and morphology) of three species of Prosopis of the Section Algarobia: P. juliflora, P. pallida, and P. limensis. Evidence for resolution of the “P. pallida–P. juliflora complex”

The problems of delimitation of species of Prosopis originate from the few morphological discontinuities which exist among some of them; some, however, originated as a result of wide distribution of germplasm without proper knowledge of the species, in particular, much material catalogued as P. juliflora, but being of other species, was distributed for reforestation projects worldwide. This work tests the morphological results obtained for P. pallida and P. limensis of the Peruvian–Ecuadorian coast and for P. juliflora of the Caribbean Basin of Colombia and Venezuela utilizing a study of AFLPs and a study of the morphology of plantlets developed in a conventional garden study. The phenogram obtained for the AFLPs demonstrates each of the three species to be a well differentiated cluster and the molecular variance between them is significantly greater than the variance within each species. Study of the plantlets also indicates statistically significant differences for four morphological characters between P. juliflora and the other two species (P. pallida and P. limensis). These results, in addition to the morphological differentiation evident between adult plants of P. pallida and P. limensis and the clear separation of these two species from P. juliflora, corroborate the genetic identity of the three taxa analyzed.     

Convergence and parallelism: is a new life ahead of old concepts?

In comparative biology, character observations initially separate similar and dissimilar characters. Only similar characters are considered for phylogeny reconstruction; their homology is attested in a two‐step process, firstly a priori of phylogeny reconstruction by accurate similarity statements, and secondly a posteriori of phylogeny analysis by congruence with other characters. Any pattern of non‐homology is then a homoplasy, commonly, but vaguely, associated with “convergence”. In this logical scheme, there is no way to analyze characters which look similar, but cannot meet usual criteria for homology statements, i.e., false similarity detected a priori of phylogenetic analysis, even though such characters may represent evolutionarily significant patterns of character transformations. Because phylogenies are not only patterns of taxa relationships but also references for evolutionary studies, we propose to redefine the traditional concepts of parallelism and convergence to associate patterns of non‐homology with explicit theoretical contexts: homoplasy is restricted to non‐similarity detected a posteriori of phylogeny analysis and related to parallelism; non‐similarity detected a priori of phylogenetic analysis and necessarily described by different characters would then correspond to a convergence event s. str. We propose to characterize these characters as heterologous (heterology). Heterology and homoplasy correspond to different non‐similarity patterns and processes; they are also associated with different patterns of taxa relationships: homoplasy can occur only in non‐sister group taxa; no such limit exists for heterology. The usefulness of these terms and concepts is illustrated with patterns of acoustic evolution in ensiferan insects. © The Willi Hennig Society 2005.     

Anticoagulation and sepsis: the opportunity for a new use of heparin?

Sepsis is a leading cause of morbidity and mortality worldwide, and the magnitude of the problem seems higher in developing countries. In the last two decades the accepted standard treatment has resulted in only a slight decrease in mortality, and that decrease has been overshadowed by an almost 300% increase in incidence. Recently has been documented the close relationship between infection, inflammation and coagulation in sepsis has been documented; and although clinically overt disseminated intravascular coagulation may occur in only 30% to 50% of septic patients, the activation of the coagulation cascade is an early and common response to the infectious challenge. Moreover most of the molecules involved in the pro-coagulant state that characterizes sepsis are also powerful generators or amplifiers of the inflammatory response. These findings have fostered a comprehensive body of research regarding biological products with anticoagulant activity, as additional therapies for patients with the most severe states of the sepsis syndrome. This review explains the biological and molecular aspects that support the potential use of anticoagulant treatments in sepsis. Furthermore, we analyze the evidence provided by experimental and pre-clinical studies, which suggest the usefulness of heparin as an effective complementary treatment throughout the clinical stages of the disease.     

Health psychology: a new form of psychotherapy?

Psychotherapy in its traditional form is being challenged due to managed care pressures. Psychotherapy using the model of health psychology can adapt well in a managed care environment. Differences between traditional psychotherapy and the psychotherapeutic approach of health psychology are discussed in this article, with a focus on an overview of health psychology and its applications to primary care, and the concept of single-session therapy. A case example of a sample treatment emphasizing the model of brief health psychology treatment is illustrated.     

The Mediterranean Quercus pyrenaica oak forest: a new habitat for the Capercaillie?

We described an extension of the known distribution range of the Cantabrian Capercaillie Tetrao urogallus cantabricus into an atypical area and habitat for the species. Nine Capercaillie leks and 14 cocks were registered in Mediterranean Quercus pyrenaica forests in an area of 1,500 km², of which 4,500 forest hectares were surveyed. At present, this population represents both the southern-most distribution for Capercaillie and the only one inhabiting Mediterranean Q. pyrenaica forests, what suggests a wider adaptation of this (sub)species than previously thought. This population and its habitat need to be better studied, as well as to be considered in conservation planning for Cantabrian Capercaillie.     

Maintenance of species identity and controlling speciation of bacteria: a new function for restriction/modification systems?

Bacteria frequently exchange DNA among each other by horizontal gene transfer. However, maintenance of species identity and in particular speciation requires a certain barrier against an unregulated uptake of foreign DNA. Here it is suggested that formation of such a barrier is one important biological function of restriction/modification systems, in addition to the classical function of protection of bacteria against bacteriophage infection. This model explains the extreme variability and wide distribution of restriction/modification systems among prokaryotes, the prevalence of RM-systems in pathogenic bacteria and the existence of several RM-systems in single bacterial strains.     

Suppression of a +1?T mutation by a nearby substitution in the mitochondrial cox1 gene of Chlamydomonas reinhardtii : a new type of frameshift suppression in an organelle genome

In Chlamydomonas reinhardtii, mutants defective in the cytochrome pathway of respiration lack the capacity to grow under heterotrophic conditions (in darkness on acetate). In the dark⁻ strain dum18, a +1 T addition in a run of four Ts, located at codon 145 of the mitochondrial cox1 gene encoding subunit I of cytochrome c oxidase, is responsible for the mutant phenotype. A leaky revertant (su11) that grows heterotrophically at a lower rate than wild-type cells was isolated from dum18. Its respiration sensitivity to cyanide was low and its cytochrome c oxidase activity was only 4% of that of the wild-type enzyme. Meiotic progeny obtained from crosses between revertant and wild-type cells inherited the phenotype of the mt ⁻ parent, showing that the suppressor mutation, like dum18 itself, is located in the mitochondrial genome. In order to map the su11 mutation relative to dum18, a recombinational analysis was performed on the diploid progeny. It demonstrated that su11 was very closely linked to the dum18 mutation – less than 20–30 bp away. The cox1 gene of the su11 revertant was then sequenced. In addition to the +1 T frameshift mutation still present at codon 145, an A → C substitution was found at codon 146, leading to the replacement of a glutamic acid by an alanine in the polypeptide chain. No other mutations were detected in the cox1 coding sequence. As the new GCG codon (Ala) created at position 146 is very seldom used in the mitochondrial genome of C. reinhardtii, we suggest that the partial frameshift suppression by the nearby substitution is due to an occasional abnormal translocation of the ribosome (+1 base shift) facilitated both by the run of Ts and the low level of weak interaction of alanyl-tRNA. Received: 27 January 1998 / Accepted: 5 May 1998     

A novel gene encoding a ras-like GTP-binding protein from Trypanosoma brucei: an evolutionary ancestor of the ras and rap genes of higher eukaryotes?

The ras superfamily of GTP binding proteins encompasses a wide range of family members, related by conserved amino-acid motifs, and act as molecular binary switches that play key roles in cellular processes. Gene duplication and divergence has been postulated as the mechanism by which such family members have evolved their specific functions. We have cloned and sequenced a ras-like gene, tbrlp, from the primitive eukaryote Trypanosoma brucei. The gene encodes a protein of 227 amino acids and contains the six conserved subdomains that designate it as a ras/rap subfamily member. However, the presence of key diagnostic residues characteristic of both the ras and rap families of GTP confuse the familial classification of this gene. Phylogenetic analysis of the GTP binding domain places its origins at the divergence point of the ras/rap families and suggests that tbrlp is an ancestral gene to the ras/rap genes of higher eukaryotes.     

Olfactory morphology of carcharhinid and sphyrnid sharks: Does the cephalofoil confer a sensory advantage?

Many hypotheses have been advanced to explain the adaptive significance of the sphyrnid cephalofoil, including potential advantages of spacing the olfactory organs at the distal tips of the broad surface. We employed comparative morphology to test whether the sphyrnid cephalofoil provides better stereo-olfaction, increases olfactory acuity, and samples a greater volume of the medium compared to the situation in carcharhiniform sharks. The broadly spaced nares provide sphyrnid species with a significantly greater separation between the olfactory rosettes, which could lead to an enhanced ability to resolve odor gradients. In addition, most sphyrnid species possess prenarial grooves that greatly increase the volume of water sampled by the nares and thus increase the probability of odorant encounter. However, despite a much greater head width, and a significantly greater number of olfactory lamellae, scalloped hammerhead sharks do not possess a greater amount of olfactory epithelial surface area than the carcharhiniform sandbar sharks. Therefore, sphyrnid sharks might not possess any greater olfactory acuity than carcharhinids. Despite this, there are clear olfactory advantages to the cephalofoil head morphology that could have led to its evolution, persistence, and diversification. persistence, and diversification.     

Global biogeography of autotroph chemistry: is insolation a driving force?

Synthesis The tissue chemistry of plants can influence ecosystem processes including growth, herbivory, and decomposition. Our comparison of nitrogen and phosphorus in over 1700 autotroph taxa demonstrates that latitudinal trends in tissue chemistry are consistent across non‐vascular and vascular species in freshwater, terrestrial, and marine ecosystems. Tissue chemistry varies most within species and taxonomic lineages, yet the nitrogen to phosphorus ratio within individuals is strikingly similar among species in different ecosystems. These results shed new light on existing hypotheses, suggesting that light (e.g. photon flux) and growing season duration are primary drivers of latitudinal gradients in tissue chemistry, but providing little support for temperature, nutrient supply, or soil substrate age. Photoautotroph nitrogen (N) and phosphorus (P) tissue concentrations can influence ecosystem function via processes including growth, decomposition, and consumption, and may reflect traits maintaining coexistence. Studies in terrestrial systems have led to hypotheses that latitudinal trends in the N and P content of leaves may be driven by soil substrate age, environmental temperature, or season length; however, terrestrial patterns alone cannot differentiate these mechanisms. Here, we demonstrate that broad geographical patterns of N and P in freshwater and marine multicellular photoautotrophs are concordant with those in terrestrial ecosystems. Our > 6800 record database reveals that mean tissue N and P increase with latitude in all ecosystems, but P increases more rapidly, causing N:P to decline; mean N:P scaling within individuals also is identical among systems, despite very different evolutionary environments. A partitioning of the variance in these data suggests that species composition and local environmental context likely lead to the variation observed within a latitudinal band. However, the consistency of trends in photosynthetic tissue chemistry across Earth’s ecosystems suggests that biogeographical gradients in insolation and growing season length may constrain tissue N and P, whereas global trends in temperature, nutrient supply, and soil substrate age are unlikely to generate the consistent latitudinal trends among ecosystems. Thus, this cross‐ecosystem comparison suggests a new hypothesis, global patterns of insolation, while also providing a new perspective on other mechanisms that have been hypothesized to underlie latitudinal trends in photosynthetic tissue chemistry.