On the origin of eukaryotic cells and their endomembranes.

A novel hypothesis for the origin of eukaryotic cells is presented. It is assumed that the universal ancestor was bounded by two membranes of heterochiral lipid composition. We propose that the prokaryotic cells (the hypothetical host entity for alpha proteic-bacteria), though sharing a common ancestor with Archaea, was bounded by two membranes. The hypothesis suggests that an alpha proteic-bacterial symbiont was enclosed in the prokaryotic cells intermembrane space. In this view, the eukaryotic nuclear membrane and endomembrane system arose from the prokaryotic cells inner membrane while the eukaryotic plasma membrane arose from the prokaryotic cells outer membrane. The outlined scenario agrees with the view that engulfment of an alpha-proteic-bacterial cell by a host entity and its transformation to a mitochondrion was the driving force leading to the appearance of the first eukaryotic cell. The hypothesis seems to be consistent with the pre-cell theory, theory of membrane heredity, and the phagocytosis-late scenario.     

Use of mitochondrial inner membrane proteins and phospholipids to facilitate disengagement of the catalytic and malonyl-CoA binding components of carnitine palmitoyltransferase from liver mitochondrial outer membranes.

1. It was shown by Ghadiminejad and Saggerson (1991) that the anionic detergent cholate caused disengagement of the malonyl-CoA binding entity from the catalytic entity of outer membrane carnitine palmitoyltransferase (CPT1). 2. This disengagement was only observed if inner membrane material was present. 3. It is now shown that this effect is mimicked by a CPT-free inner membrane protein fraction together with an inner membrane lipid extract or with individual phospholipids (phosphatidylcholine, phosphatidylethanolamine or diphosphatidylglycerol). 4. The lipids alone have no effect but act synergistically with the inner membrane protein fraction.     

A novel homothallic variety of Agaricus bisporus comprises rare tetrasporic isolates from Europe

Among 400 wild specimens of A. bisporus collected in Europe, only three were tetrasporic. In the case of two of them from France, a previous study showed that one was homokaryotic and hypothetically belonged to a homothallic entity while the other was heterokaryotic and possibly resulted from hybridization between a member of this entity and a classical bisporic strain. A third tetrasporic specimen recently was discovered in Greece. Morphological and genetic comparisons, using alloenzymatic markers, molecular markers and ITS polymorphisms, reveal that this third specimen is homokaryotic and belongs, with the homokaryotic specimen from France, to the same entity. Dissimilarity analysis confirms the hybrid origin of the heterokaryotic specimen. Varietal status is proposed for this homothallic, highly homogeneous entity, and A. bisporus var. eurotetrasporus is described. This novel variety clearly differs from var. bisporus by its tetrasporic basidia and from var. burnettii by its longer spores. It has a complex story because it can interbreed with var. bisporus and shares the same habitat; however, because of its homothallic life cycle and its partial intersterility, it is probably in the process of speciation.     

Entity Normalization in Life Cycle Assessment: Hybrid Schemes Applied to a Transportation Agency Case Study

Government agencies, companies, and other entities are using environmental assessments, like life cycle assessment (LCA), as an input to decision‐making processes. Communicating the esoteric results of an LCA to these decision makers can present challenges, and interpretation aids are commonly provided to increase understanding. One such method is normalizing results as a means of providing context for interpreting magnitudes of environmental impacts. Normalization is mostly carried out by relating the environmental impacts of a product (or process) under study to those of another product or a spatial reference area (e.g., the United States). This research is based on the idea that decision makers might also benefit from normalization that considers comparisons to their entity's (agency, company, organization, etc.) total impacts to provide additional meaning and aid in comprehension. Two hybrid normalization schemes have been developed, which include aspects of normalization to both spatially based and entity‐based impacts. These have been named entity‐overlaid and entity‐accentuated normalization, and the schemes allow for performance‐based planning or emphasizing environmental impact types that are most relevant to an entity's operational profile, respectively. A hypothetical case study is presented to demonstrate these schemes, which uses environmental data from a U.S. transportation agency as the basis for entity normalization factors. Results of this case study illustrate how entity‐related references may be developed, and how this additional information may enhance the presentation of LCA results using the hybrid normalization schemes.     

2 A prebiotic RNA apparatus functions within the contemporary ribosome

Ribosomes, the universal cellular machines, possess spectacular architecture accompanied by inherent mobility, allowing for their smooth performance as polymerases that translate the genetic code into proteins. The site for peptide bond formation is located within a universal internal semi-symmetrical region, which was identified within all contemporary ribosomes. The high conservation of this region implies its existence irrespective of environmental conditions and indicates that it may represent an ancient RNA molecular apparatus. Hence, we named it the “proto-ribosome”. This prebiotic pocket-like RNA entity is suggested to be capable to accommodate substrates whose stereochemistry enables the creation of chemical bonds. It could have evolved from an earlier catalytic RNA entity that we named the “pre-proto-ribosome”, presumed to be a molecular machine capable of performing various essential tasks in the RNA world, which was snatched by the amino acid invaders for producing proteins.     

A new orchid Paphiopedilum guangdongense and its molecular evidence

A new Paphiopedilum entity found in southern Guangdong was studied taxonomically by means of internal transcribed spacer of nuclear ribosomal DNA analysis in addition to morphological and phytogeographical considerations. This entity is similar to Paphiopedilum gratrixianum (Masters) Rolfe morphologically, from which it differs by having narrower leaves not wider than 2 cm and lacking purple spots toward abaxial base, pale green dorsal sepal veined with pale purplish brown and not heavily spotted with purple, and staminode subtruncate and mucronate at apex. An analysis of internal transcribed spacer sequences of this entity and its allies came to the same conclusion that the entity is a member of Paphiopedilum section Paphiopedilum and closely related to but distinct from P. gratrixianum. As a result, it is treated here as a new species, Paphiopedilum guangdongense Z.J. Liu & L.J.Chen.     

Adaptedness, evolution and a hierarchical concept of fitness.

Fitness is a consequence of the adaptedness of an entity to its environment. The fitness of an evolutionary entity, when the entity is defined by a set of attributes determining how it interacts with its environment, is manifested as persistence of those attributes. Two measures of fitness are presented to explicate this concept: (1) an extensive measure of the persistence of the original set of attributes in the individual entity and its descendants, but corrected for evolution; this includes as a special case fitness as used in population genetics; and, (2) an intensive measure that is independent of the abundance of descendant exemplars. Fitness as conceived here is a function of survival time, degree of evolution, and when applicable, reproductive contribution. The rate of fitness increase of an entity will vary inversely with the degree of evolutionary change experienced by the entity, its descendants, or both through time. Adaptive evolution can increase the length of time that fitness accumulates by increasing the survival of descendants possessing all or some of the ancestral attributes. Reproduction, where possible, can increase the number of descendants. This concept of fitness is simple, unambiguous, coherent, and applicable to entities at any hierarchical level of interest to ecologists and evolutionary biologists.     

Primary leiomyosarcoma of the inferior vena cava presenting as a renal mass

Leiomyosarcoma of the inferior vena cava (IVC) is an extremely rare entity. We present the case of a 62-year-old woman who was found to have a large right upper quadrant mass upon examination by her primary care physician in evaluation for diffuse abdominal pain accompanied by anorexia and weight loss. A computed tomographic scan and magnetic resonance imaging demonstrated a 13-cm retroperitoneal lesion that appeared to stem from the right kidney and yielded a tumor thrombus up to the level of the hepatic venous confluence. The patient underwent a right radical nephrectomy and IVC thrombectomy for treatment of a presumed renal cell carcinoma. Instead, pathology revealed the tumor to be a leiomyosarcoma of the IVC. We document this unusual presentation of an extremely rare tumor entity.     

Characterization of content and chromatographic forms of neuropeptides in purified nerve varicosities prepared from guinea pig myenteric plexus

Partially purified nerve varicosities (PV) prepared from guinea pig ileal myenteric plexus were found to contain, by radioimmunoassay, gastrin-releasing polypeptide (GRP), substance P (SP), galanin, Leu-enkephalin (LE), Met-enkephalin (ME), and vasoactive intestinal polypeptide (VIP). SP was present in the highest concentration followed by, in descending order, ME, LE, VIP, GRP and galanin. On reverse-phase HPLC, SP-, LE- and ME-like immunoreactivity in the PV preparation eluted at retention times similar to their synthetic analogues, galanin-like immunoreactivity eluted at a retention time different from that of synthetic porcine galanin and VIP-like immunoreactivity eluted at the retention time of synthetic guinea pig VIP. GRP-like immunoreactivity, on reverse-phase HPLC, eluted at retention times close to that of synthetic porcine GRP-(1-27) and its major oxidized form. Evidence was obtained for the presence of an alpha-neurokinin-like immunoreactive entity and an unidentified SP-like immunoreactive entity in guinea pig myenteric plexus.     

Greenization of Venture Capital and Green Innovation of Chinese Entity Industry

Based on literature review, firstly, the work analyzed the necessity and main features of venture capital promoting green innovation of entity industry. Greenization of venture capital was the key to promote green innovation of entity industry. Secondly, the mechanism that venture capital promoted green innovation of entity industry was analyzed through model construction. The results showed that construction of ecological civilization as well as market competition and regulations were preconditions of transforming ordinary venture capital into green venture capital; they were also the precondition of venture capital promoting green innovation of entity industry. Thirdly, theoretical and empirical studies were conducted on effects of venture capital for green innovation of entity industry. Recommendations were proposed for venture capital to promote green innovation of entity industry. Empirical studies showed that venture capital could more effectively enhance the green innovation capacity of Chinese entity industry than bank loans. To exert the role of venture capital in green innovation of entity industry, the development of venture capital should be accelerated in a larger scale. Meanwhile, Chinese venture capital industry should be promoted for green transformation, thus more venture capital can be transformed into green venture capital.     

Integration, individuality and species concepts

Integration (interaction among parts of an entity) is suggested to be necessary for individuality (contra, Metaphysics and the Origin of Species). A synchronic species is an integrated individual that can evolve as a unified whole; a diachronic lineage is a non-integrated historical entity that cannot evolve. Synchronic species and diachronic lineages are consequently suggested to be ontologically distinct entities, rather than alternative perspectives of the same underlying entity (contra Baum (1998), Syst. Biol. 47, 641–653; de Queiroz (1995), Endless Forms: Species and Speciation, pp. 57–75; Genes, Categories and Species). Species concepts usually refer to either one or the other entity; for instance, the Biological Species Concept refers to synchronic species, whereas the Cladistic Species Concept refers to diachronic lineages. The debate over species concepts has often failed to recognise this distinction, resulting in invalid comparisons between definitions that attempt to delineate fundamentally different entities. This revised version was published online in July 2006 with corrections to the Cover Date.     

Extracellular localization of a nonfimbrial hemagglutinin of Yersinia pseudotuberculosis.

A nonfimbrial hemagglutinin (HA) of Yersinia pseudotuberculosis was observed by immunoelectron microscopy using monospecific HA antiserum and protein A-gold conjugate. The HA, an amorphous but morphologically identifiable entity, was located in a region distal to or detached from the outer edge of bacteria.     

Free nonimmobilized ligands as a tool for purification of proteins

Purification of proteins on a large scale is a complex multistep process, and alternative economic strategies are required. This study presents a novel approach (Affinity Sinking, AS) for purification of native proteins utilizing nonimmobilized modified ligands. The nonimmobilized state of the ligand circumvents the need for immobilizing ligands to polymeric supports. Therefore, purification from large volumes can be accomplished without the use of industrial-scale affinity columns. The mechanism of product capture is formation and precipitation of a specific [target-protein/modified-ligand] complex by using a soluble interconnecting entity that generates an insoluble [target-protein/modified-ligand/interconnecting entity] sediment containing the target protein. Rabbit IgG and two glycoproteins were purified accordingly, utilizing free avidin (as the interconnecting entity) and either desthiobiotinylated-protein A (DB-ProA) or desthiobiotinylated-concanavalin A (DB-ConA) as the modified ligand. The recovery yields for the IgG and the two glycoproteins were 80-86% and 70-75%, respectively. Target proteins are eluted from the generated pellet nearly without disrupting the [modified-ligand/interconnecting entity] macro-complex, thus enabling a practical procedure of recovering target proteins. Leaching of the DB-ProA ligand under eluting conditions (pH 3) was found to be lower than 1%. The two modified ligands, DB-ProA and DB-ConA, were regenerated without any chromatographic procedure in 80% and 85%-89% yield, respectively. The advantage of excluding the polymeric component from the purification process and obtaining highly purified proteins has been demonstrated, and it implies that other contaminants (e.g. endotoxins, prions, host DNA) could be excluded as well, thereby reducing the number of purification steps in a typical downstream process.     

Causal Characteristics for Ecoepidemiology

We suggest that there are six fundamental characteristics of causation: time order, co-occurrence, preceding causation, sufficiency, interaction, and alteration. The cause precedes the effect (time order). The cause co-occurs with the unaffected entity in space and time (co-occurrence). Causes and their effects are the result of a web of causation (preceding causation). The intensity, frequency, and duration of the cause are adequate and the susceptible entity can exhibit the type and magnitude of the effect (sufficiency). The cause effectively interacts with the entity in a way that induces the effect (interaction). And, the entity is changed by the interactions with the cause (alteration). In contrast to Hill's criteria, the causal characteristics are distinct from the: (1) evidence that is used to document causal characteristics, (2) sources of information used to develop the evidence, and (3) qualities used to evaluate evidence of causal characteristics and body of evidence for the causal relationship. Evidence of causal characteristics can form the basis for assessments of epidemiological studies and can structure an explanatory narrative that is causally relevant and substantive. Six core characteristics may be easier to organize, evaluate, communicate, and for decision-makers to assimilate, remember, and inspire action.     

Comprehensive phylogenetic analyses of the Ruppia maritima complex focusing on taxa from the Mediterranean

Recent molecular phylogenetic studies reported high diversity of Ruppia species in the Mediterranean. Multiple taxa, including apparent endemics, are known from that region, however, they have thus far not been exposed to phylogenetic analyses aimed at studying their relationships to taxa from other parts of the world. Here we present a comprehensive phylogenetic analyses of the R. maritima complex using data sets composed of DNA sequences of the plastid genome, the multi-copy nuclear ITS region, and the low-copy nuclear phyB gene with a primary focus on the Mediterranean representatives of the complex. As a result, a new lineage, “Drepanensis”, was identified as the seventh entity of the complex. This lineage is endemic to the Mediterranean. The accessions included in the former “Tetraploid” entity were reclassified into two entities: an Asia–Australia–Europe disjunct “Tetraploid_α” with a paternal “Diploid” origin, and a European “Tetraploid_γ” originating from a maternal “Drepanensis” lineage. Another entity, “Tetraploid_β”, is likely to have been originated as a result of chloroplast capture through backcrossing hybridization between paternal “Tetraploid_α” and maternal “Tetraploid_γ”. Additional discovery of multiple tetraploidizations as well as hybridization and chloroplast capture at the tetraploid level indicated that hybridization has been a significant factor in the diversification of Ruppia.     

Fluorophore(s) Appended Fullerene Dyads and Triads for Probing Photoinduced Energy Transfer: Syntheses, Electronic Structure, and Fluorescence Studies

Fullerene, C₆₀ was functionalized to possess one or two fluorophore entities. The fluorophore–fullerene dyads thus synthesized contain either a naphthalene, pyrene, or fluorene entity while the triads contain either a pyrene or fluorene entity in addition to a naphthalene entity. The redox behavior of these dyads and triads were probed by cyclic voltammetric technique, while the geometry and electronic structures were deduced from ab initio B3LYP/3-21G(*) method. Steady-state emission studies revealed the occurrence of energy transfer from the singlet excited fluorophore to the fullerene entity in the case of the dyads while the occurrence of step-by-step sequential energy transfer is envisioned in the case of the triads. A better ‘antenna-effect’ owing to the extended range of excitation wavelength to induce energy transfer to the appended fullerene has been achieved in the case of the triads.     

Study of Two Bacteriophages of Bacillus stearothermophilus Strain NCA1518

Studies of bacteriophages GH5 and GH8 of Bacillus stearothermophilus strain NCA1518 revealed that their properties were sufficiently different from known phages and from each other to indicate that each was a different entity, although no major deviation was demonstrated.     

Using workflows to explore and optimise named entity recognition for chemistry

Chemistry text mining tools should be interoperable and adaptable regardless of system-level implementation, installation or even programming issues. We aim to abstract the functionality of these tools from the underlying implementation via reconfigurable workflows for automatically identifying chemical names. To achieve this, we refactored an established named entity recogniser (in the chemistry domain), OSCAR and studied the impact of each component on the net performance. We developed two reconfigurable workflows from OSCAR using an interoperable text mining framework, U-Compare. These workflows can be altered using the drag-&-drop mechanism of the graphical user interface of U-Compare. These workflows also provide a platform to study the relationship between text mining components such as tokenisation and named entity recognition (using maximum entropy Markov model (MEMM) and pattern recognition based classifiers). Results indicate that, for chemistry in particular, eliminating noise generated by tokenisation techniques lead to a slightly better performance than others, in terms of named entity recognition (NER) accuracy. Poor tokenisation translates into poorer input to the classifier components which in turn leads to an increase in Type I or Type II errors, thus, lowering the overall performance. On the Sciborg corpus, the workflow based system, which uses a new tokeniser whilst retaining the same MEMM component, increases the F-score from 82.35% to 84.44%. On the PubMed corpus, it recorded an F-score of 84.84% as against 84.23% by OSCAR.