Causality, randomness, intelligibility, and the epistemology of the cell

Because the basic unit of biology is the cell, biological knowledge is rooted in the epistemology of the cell, and because life is the salient characteristic of the cell, its epistemology must be centered on its livingness, not its constituent components. The organization and regulation of these components in the pursuit of life constitute the fundamental nature of the cell. Thus, regulation sits at the heart of biological knowledge of the cell and the extraordinary complexity of this regulation conditions the kind of knowledge that can be obtained, in particular, the representation and intelligibility of that knowledge. This paper is essentially split into two parts. The first part discusses the inadequacy of everyday intelligibility and intuition in science and the consequent need for scientific theories to be expressed mathematically without appeal to commonsense categories of understanding, such as causality. Having set the backdrop, the second part addresses biological knowledge. It briefly reviews modern scientific epistemology from a general perspective and then turns to the epistemology of the cell. In analogy with a multi-faceted factory, the cell utilizes a highly parallel distributed control system to maintain its organization and regulate its dynamical operation in the face of both internal and external changes. Hence, scientific knowledge is constituted by the mathematics of stochastic dynamical systems, which model the overall relational structure of the cell and how these structures evolve over time, stochasticity being a consequence of the need to ignore a large number of factors while modeling relatively few in an extremely complex environment.     

Expression, localization, structural, and functional characterization of pFGE, the paralog of the Calpha-formylglycine-generating enzyme

pFGE is the paralog of the formylglycine-generating enzyme (FGE), which catalyzes the oxidation of a specific cysteine to Calpha-formylglycine, the catalytic residue in the active site of sulfatases. The enzymatic activity of sulfatases depends on this posttranslational modification, and the genetic defect of FGE causes multiple sulfatase deficiency. The structural and functional properties of pFGE were analyzed. The comparison with FGE demonstrates that both share a tissue-specific expression pattern and the localization in the lumen of the endoplasmic reticulum. Both are retained in the endoplasmic reticulum by a saturable mechanism. Limited proteolytic cleavage at similar sites indicates that both also share a similar three-dimensional structure. pFGE, however, is lacking the formylglycine-generating activity of FGE. Although overexpression of FGE stimulates the generation of catalytically active sulfatases, overexpression of pFGE has an inhibitory effect. In vitro pFGE interacts with sulfatase-derived peptides but not with FGE. The inhibitory effect of pFGE on the generation of active sulfatases may therefore be caused by a competition of pFGE and FGE for newly synthesized sulfatase polypeptides.     

Checklist of the species of the aseptate gregarine families Aikinetocystidae,Diplocystidae, Allantocystidae,Schaudinnellidae, Ganymedidae,and Enterocystidae

The genera and species in six families of the eugregarine suborder Aseptatorina Chakravarty, 1960, are reviewed and the presently accepted ones are listed: Aikinetocystidae Bhatia, 1930 (two genera and two species); Diplocystidae Bhatia, 1930 (one genus and eight species); Allantocystidae tocystidae Bhatia, 1930 (one genus and one species); Schaudinnellidae Poche, 1913 (one genus and one species); Ganymedidae Huxley, 1910 (one genus and one species); and Enterocystidae Codreanu, 1940 (one genus and eight species). A list of 22 synonyms and lapsi calami is also given. Species which might be of value in the biological control of disease vectors are indicated.     

A comparative histochemical study of the masseter muscle of the cattle,sheep, swine,dog, guinea pig,and rat

Summary The masseter muscles of different mammals were studied by means of histochemical reactions: NADH: Nitro BT oxidoreductase (NADHOX), 3-hydroxybutyrate: NAD⁺ oxidoreductase (HBOX), glycerol-3-phosphate: menadione oxidoreductase (GPOX), and acid-stable and alkali-stable myosin adenosine triphosphatase (ATPase). The masseter muscles of cattle and sheep consisted only of the fibres that reacted moderately for GPOX and strongly for NADHOX, HBOX, and the acid-stable ATPase. The masseter fibres of rats and guinea pigs reacted uniformly and strongly for GPOX and the alkali-stable ATPase. The fibres of the rats showed a weak to strong reaction for NADHOX and mostly a negative reaction for HBOX, whereas those of the guinea pigs reacted uniformly and strongly for NADHOX and HBOX. The masseter fibres of swine and dogs showed a weak or strong reaction for the alkali-stable and a negative or weak reaction for HBOX. The fibres of the swine were weak to strong in NADHOX activity and those of the dogs uniformly strong; the fibres of the two species gave a moderate to strong reaction for GPOX. The masseter fibres of the ruminant differed from those of the other species in histochemical properties, and appeared to have the histochemical characteristics that meed functional demands for slow, long-term exercise.     

Making Forest of Bliss: The Film, the Book, the DVD, and the Breakthrough

Robert Gardner's and Àkos Östör's Making of Forest of Bliss (2002) is a combination book and DVD that contains eight teaching tools for better understanding Gardner's celebrated film Forest of Bliss. After the film was shot in 1985, filmmaker Gardner and anthropologist Östör recorded a conversation about each image and sound of the film while they screened it again in 1987, and remembered their filmmaking process on location in Benares, India. The feature length (89 minute) documentary about death ritual, reincarnation, the sacred Ganges River, and the very atmosphere of Benares is included as DVD, as are teaching tools such as frame grabs (still images from the film), a mathematically precise shot list, bibliography, important criticism and essays about the film, and the featured in-depth conversation between filmmaker Gardner and anthropological advisor Östör. This essay articulates the unique breakthroughs in pedagogy, cross-cultural studies, and multidisciplinary analysis such hybrid technology provides.     

Ultrastructure,Behavior, and Algal Flagellate Affinities of the Helioflagellate Ciliophrys marina,and the Classification of the Helioflagellates (Protista,Actinopoda, Heliozoea)1

Ciliophrys marina is a small marine helioflagellate, with a central nucleus, which is capable of reversibly transforming from a rapidly swimming flagellate cell with no axopodia to the structure of a heliozoan with a flagellum that beats only a few times a minute. When in the flagellate form, the flagellum acts as a tractellum due to the tubular mastigonemes found along its length. When the rapidly swimming flagellate strikes a piece of debris, the flagellum goes through a very characteristic shock-induced avoidance reaction. Similarly, when a mechanical shock is delivered to the cell in its heliozoan form, the axopodia are contracted in less than 20 msec. Both reactions are inhibited in low calcium seawater. Transformation from the heliozoan to the flagellate form is accomplished by slow retraction and absorbance of the axopodia and activation of the flagellum. Ultrastructurally, each axopodium is found to contain three microtubules which attach to the outer nuclear membrane of the central nucleus at sites that this study characterizes by electron microscopy of thin sections and freeze fracture preparations. The mitochondria have tubular cristae, each containing an intracristal filament. Finally, a taxonomic review of the helioflagellates is presented, and it is suggested that C. marina is derived from the chrysomonads. An argument is also made for classifying C. marina with the heliozoan order Actinophryida, as a recently published classification of the protozoa does.     

Functional characterization of the promoter of the vitellogenin gene, AsVg1, of the malaria vector, Anopheles stephensi

Some genetic strategies for controlling transmission of mosquito-borne diseases call for the introgression of antipathogen effector genes into vector populations. Endogenous mosquito promoter and other cis-acting DNA sequences are needed to direct the expression of the effector molecules to maximize their efficacy. Vitellogenin (Vg)-encoding gene control sequences are candidates for driving tissue-, stage- and sex-specific expression of exogenous genes. One of the Anopheles stephensi Vg genes, AsVg1, was cloned and a full-length cDNA, as well as 850 base pairs adjacent to the 5'-end, were sequenced and characterized. Expression of AsVg1 is restricted to the fat body tissues of blood-fed females, and the amino acid sequence of the conceptual translation product is >85% identical to those of other anopheline Vgs. These characteristics support the conclusion that AsVg1 is a Vg-encoding gene. Functional analyses of the AsVg1 putative cis-regulatory sequences were performed using transgenic mosquitoes. The results showed that DNA fragments encompassing the 850 base pairs immediately adjacent to the 5'-end of the gene and the 3'-end untranslated region are sufficient to direct sex-, stage- and tissue-specific expression of a reporter gene. These data indicate that the AsVg1 promoter is a good candidate for controlling the expression of anti-pathogen effector molecules in this malaria vector mosquito.     

Solubility, adsorption, and the thermodynamics of the cutoff effect

For many years, the expression "cutoff effect of anesthesia," has been used to denote the failure of the higher alcohols or paraffins to produce anesthesia. As such, it is used to assess the plausibility of specific models, proposed for anesthesia. However, the uses were shown, in many respects, to be problematic. This article augments the notion of the cutoff to fit for all cases in which only some of the molecules in a homologous series are anesthetics. We find that the location of the cutoff points is affected by three free energy quantities: that of the adsorption of the agent to the anesthetic "site" (f(sl,site)), that of the perturbation of the site (f(ll,site)), and that of the evaporation of the agent from its pure condensed phase (Deltamu degrees (evaporation)). This outcome indicates that the cutoff cannot be attributed to a single parameter. In addition, the analyses that attribute the cutoff to the failure of compounds to obey the much-used Meyer-Overton correlation will have to be amended. This article shows that cutoff results can be used to elucidate the structure of a site.     

Quantitation of the involvement of the recA, recB, recC, recF, recJ, recN, lexA, radA, radB, uvrD, and umuC genes in the repair of X-ray-induced DNA double-strand breaks in Escherichia coli

Isogenic Escherichia coli strains carrying single DNA-repair mutations were compared for their capacity for (i) the repair of X-ray-induced DNA double-strand breaks (DSB) as measured using neutral sucrose gradients; (ii) medium-dependent resistance, i.e., a recA-dependent X-ray survival phenomenon that correlates closely with the capacity for repairing DSB; and (iii) the growth medium-dependent, recA-dependent repair of X-ray-induced DNA single-strand breaks (SSB) as measured using alkaline sucrose gradients (about 80% of these SSB are actually parts of DSB). These three capacities were measured to quantitate more accurately the involvement of the various genes in the repair of DSB over a wide dose range. The mutations tested were grouped into five classes according to their effect on the repair of X-ray-induced DSB: (I) the recA, recB, recC, and lexA mutants were completely deficient; (II) the radB and recN mutants were about 90% deficient; (III) the recF and recJ mutants were about 70% deficient; (IV) the radA and uvrD mutants were about 30% deficient; and (V) the umuC mutant resembled the wild-type strains in its capacity for the repair of DSB.     

Pyrin, product of the MEFV locus, interacts with the proapoptotic protein, Siva

Mutations in pyrin cause the autoinflammatory disorder familial Mediterranean fever (FMF), a syndrome characterized by sporadic and unpredictable attacks of fever and localized severe pain. Currently, it is not clear how attacks are triggered, nor why they spontaneously resolve after 2 or 3 days. In fact, the cellular function of the pyrin protein and the molecular underpinnings of its malfunction in FMF have so far eluded clear definition. The identification of pyrin-interacting proteins has the potential to increase our understanding of the cellular networks in which pyrin functions. Previous reports have established that pyrin interacts with the apoptotic protein ASC, the cytoskeletal adaptor protein PSTPIP1, the inflammatory caspase, Caspase-1 and certain forms of the cytosolic anchoring protein 14-3-3. Here, we report that pyrin also interacts with Siva, a pro-apoptotic protein first identified for its interaction with the cytosolic tail of CD27, a TNF family receptor. The interaction between pyrin and Siva involves the C-terminal B30.2/rfp/SRPY domain of pyrin and exon 1 of Siva. We show that Siva and pyrin are indeed co-expressed in human neutrophils, monocytes, and synovial cells. Furthermore, using a novel protein/protein interaction assay, we demonstrate that pyrin can recruit Siva to ASC specks, establishing a potential platform for intersection of ASC and Siva function. Finally, we show that pyrin modulates the apoptotic response to oxidative stress mediated by Siva. Thus, the Siva-pyrin interaction may be a potential target for future therapeutic strategies.     

Fate of bacteria, Aeromonas caviae, in the midgut of the housefly, Musca domestica

Abstract. The role of houseflies as agents in the spread of bacterial diseases has been thoroughly investigated, yet the fate of bacteria ingested by flies has not. We examined the physical location of the bacterial enteropathogen Aeromonas caviae in the midgut of laboratory‐reared adult houseflies. Food ingested by houseflies was separated from the midgut epithelium by a double‐layered peritrophic matrix (PM). The inner PM intimately enveloped the food as fecal pellets (food boluses), while the outer PM appeared as a long continuous tube. In flies fed a suspension of A. caviae, live bacteria were not observed within the inner PM, but were compartmentalized between folds of the PM in the inter‐PM space. Similar observations were made for flies fed a suspension of Serratia liquefaciens and for highly contaminated feral flies. Isolates of both A. caviae and S. liquefaciens were chitinolytic (as demonstrated by clearing zones on chitin agar), but the potential role of bacterial enzymes in the alteration of PM morphology or formation needs further investigation.     

On the ability of four flavonoids, baicilein, luteolin, naringenin, and quercetin, to suppress the fenton reaction of the iron-ATP complex

Four flavonoids, baicilein, luteolin, naringenin, and quercetin were investigated for their ability to suppress the Fenton reaction characteristic of the iron-ATP complex. Absorption spectroscopy indicates that under the conditions of 18.75% aqueous methanol, 0.0625 mM HEPES pH 7.4 buffer and 1.5:1 quercetin/iron-ATP ratio a mix ligand complex formed. All four flavonoids were found to interfere with the voltammetric catalytic wave associated with the iron-ATP complex in the presence of H₂O₂. Quercetin and luteolin were able to completely suppress the catalytic wave of the iron-ATP/H₂O₂ system when a minimum ratio of 1.5:1 of the flavonoid to iron-ATP was reached. At this ratio, the ability of the studied series of flavonoids to suppress the Fenton reaction characteristic of iron-ATP follows as quercetin luteolin > naringenin baicilein. Both quercetin and luteolin contain catechol on the B ring, which may enhance the iron chelation of these species over baicilein and naringenin. The common structural feature of all of these flavonoids is the 4-keto, 5-hydroxy region, which may also contribute to the chelation of iron.     

Observations on the biology of the perch, Perca fluviatilis, in the River Stour, Dorset

SUMMARY. Opercular bones from 323 perch from the River Stour were used for age and back-calculated growth determinations. Annuli were formed during May at the beginning of the growth period. Growth was minimal from October to April. Female perch grew faster than males, and the growth rates of both sexes were higher than those observed in most other European waters. Spawning occurred during late April and early May; male gonads began development in August and had attained their maximum weight in September, but the ovaries developed gradually from August until April. Immature perch had an annual cycle of condition with a maximum in June-July and a minimum in December-January. The condition of mature males and females was affected by the gonad cycle. The fecundity of Stour perch is expressed by the formula: log egg number = 2.40 log length (mm) - 1.34.
Approximately 25% of males were mature at age I and all were mature at age II, whereas most females did not spawn until age III. Ephemeroptera nymphs and minnow fry constituted the bulk of the diet of 0-group perch; Ephemeroptera nymphs, minnow fry and Corixidae were the most numerous items in I group perch, whereas older perch contained Corixidae and a wider range of fish prey species, although minnows were the most numerous of these.     

Age, growth, maturity, and mortality of the Alaska skate, Bathyraja parmifera, in the eastern Bering Sea

The Alaska skate, Bathyraja parmifera, is the most abundant species of skate on the eastern Bering Sea shelf, accounting for over 90% of total skate biomass. However, little is known regarding the life history of this species despite its common occurrence as bycatch in several Bering Sea fisheries. This is the first study to focus on the age and growth of B. parmifera. From 2003 to 2005, more than one thousand specimens were collected by fisheries observers and on scientific groundfish surveys. Annual banding patterns in more than 500 thin sections of vertebral centra were examined for age determination. Caudal thorns were tested as a potentially non-lethal ageing structure. Annual band pair deposition was verified through edge and marginal increment analyses. A three-parameter von Bertalanffy growth function and a Gompertz growth function were fit to observed length-at-age data. Both models provided significant fits, although the Gompertz function best described the overall pattern of growth in both males and females, based upon statistical criteria and parameter estimates. Age and size at 50% maturity were 9 years and 92 cm TL for males and 10 years and 93 cm TL for females. The maximum observed ages for males and females were 15 years and 17 years, respectively. Estimates of natural mortality (M) ranged from 0.14 to 0.28, and were based on published relationships between M and longevity, age at maturity, and the von Bertalanffy growth coefficient. Due to these life history characteristics and a lack of long-term species-specific stock data, a conservative management approach would be appropriate for B. parmifera.     

Fecundity,autogeny, and the larval environment of the pitcher-plant mosquito,Wyeomyia smithii

Summary Pupae and fourth instar larvae of a southern (30°N, Alabama, USA) population of Wyeomyia smithii Coq. (Diptera: Culicidae) were collected from pitcher plants. Adults which emerged were maintained without food then dissected to determine their egg clutch size. Among females which matured eggs, fecundities were negatively correlated with larval densities in individual pitchers. The mean autogenous fecundity of the overwintering generation did not differ from a summer sample. Adults unable to mature eggs comprised 6–39% of samples, depending on whether collected as pupae or fourth instar larvae. Fecundity was negatively correlated with time to adult eclosion among larvae maintained on unrenewed pitcher contents in the laboratory.Cohorts from this population were reared in artificial containers from egg hatch to adulthood at a single density and a superior or inferior diet. On the superior larval diet, all females survived to reproductive age, and all but one (>99%) produced eggs autogenously. On the inferior diet, survivorship to adult eclosion was significantly less, a high proportion of females died before reaching reproductive age, and only 19% of survivors matured eggs without blood. Protracted larval development induced by the inferior diet did not influence the probability of autogeny among females that survived to reproductive maturity.The relationship between larval environment and reproductive strategies is contrasted across the geographic range of W. smithii. Bloodfeeding occurs among southern populations where density dependent constraints on preimaginal growth are constantly severe. The loss of hematophagy among northern populations may have been facilitated by periods of density independent larval growth.Institute of Food and Agricultural Sciences, University of Florida, Experimental Station Journal Series No. 3645     

The helminth community of the wood mouse, Apodemus sylvaticus, in the Sierra Espuna, Murcia, Spain

The helminth community of the wood mouse, Apodemus sylvaticus, in the Sierra Espuna was characterized after a complete analysis of its helminth community component and infracommunity structure relative to host age, sex and year of capture. The helminth community comprised 13 species: one trematode, four cestodes and eight nematodes. The cestode Pseudocatenotaenia matovi and the nematode Syphacia frederici were the most prevalent and abundant helminth species, respectively. Sixty four percent of mice analysed presented helminths with a direct cycle and 42% presented helminths with an indirect cycle. The helminth community presents a low diversity with infracommunities usually made up of only one or two helminth species. Host age and year of capture seem to play a major role in determining species richness and helminth diversity, but not in determining the abundance of helminths. Host sex does not seem to affect the infection rate nor the diversity. Further studies on more samples of wood mice and other small mammal species in this regional park are needed to explore any possible interactions between helminth communities in the host populations.     

The parasitic chytrid, Zygorhizidium, facilitates the growth of the cladoceran zooplankter, Daphnia, in cultures of the inedible alga, Asterionella

In food-web studies, parasites are often ignored owing to their insignificant biomass. We provide evidence that parasites may affect trophic transfer in aquatic food webs. Many phytoplankton species are susceptible to parasitic fungi (chytrids). Chytrid infections of diatoms in lakes may reach epidemic proportions during diatom spring blooms, so that numerous free-swimming fungal zoospores (2-3 microm in diameter) are produced. Analysis shows that these zoospores are rich in polyunsaturated fatty acids and sterols (particularly cholesterol), which indicates that they provide excellent food for zooplankters such as Daphnia. In life-table experiments using the large diatom Asterionella formosa as food, Daphnia growth increased significantly in treatments where a parasite was present. By grazing on the zoospores, Daphnia acquired important supplementary nutrients and were able to grow. When large inedible algae are infected by parasites, nutrients within the algal cells are consumed by these chytrids, some of which, in turn, are grazed by Daphnia. Thus, chytrids transfer energy and nutrients from their hosts to zooplankton. This study suggests that parasitic fungi alter trophic relationships in freshwater ecosystems and may be the important components in shaping the community and the food-web dynamics of lakes.     

A comparative histochemical study of the masseter muscle of the cattle, sheep, swine, dog, guinea pig, and rat.

The masseter muscles of different mammals were studied by means of hisotchemical reactions: NADH: Nitro BT oxidoreductase (NADHOX), 3-hydroxybutyrate: NAD+ oxidoreductase (HBOX), glycerol-3-phosphate: menadione oxidoreductase (GPOX), and acid-stable and alkali-stable myosin adenosine triphosphatase (ATPase). The masseter mucles of cattle and sheep consisted only of the fibres that reacted moderately for GPOX and strongly for NADHOX, HBOX, and the acid-stable ATPase. The masseter fibres of rats and guinea pigs reacted uniformly and strongly for GPOX and the alkali-stable ATPase. The fibres of the rats showed a weak to strong reaction for NADHOX and mostly a negative reaction for HBOX, whereas those of the guinea pigs reacted uniformly and strongly for NADHOX and HBOX.The masseter fibres of swine and dogs showed a weak or strong reaction for the alkali-stable and a negative or weak reation for HBOX. The fibres of the swine were weak to strong in NADHOX activity and those of the dogs uniformly strong; the fibres of the two species gave a moderate to strong reaction for GPOX. The masseter fibres of the ruminant differed from those of the other species in histochemical properties, and appeared to have the histochemical characteristics that meed functional demands for slow, long-term exercise.     

Methane, oxygen, photosynthesis, rubisco and the regulation of the air through time

Rubisco I's specificity, which today may be almost perfectly tuned to the task of cultivating the global garden, controlled the balance of carbon gases and O(2) in the Precambrian ocean and hence, by equilibration, in the air. Control of CO(2) and O(2) by rubisco I, coupled with CH(4) from methanogens, has for the past 2.9 Ga directed the global greenhouse warming, which maintains liquid oceans and sustains microbial ecology.Both rubisco compensation controls and the danger of greenhouse runaway (e.g. glaciation) put limits on biological productivity. Rubisco may sustain the air in either of two permissible stable states: either an anoxic system with greenhouse warming supported by both high methane mixing ratios as well as carbon dioxide, or an oxygen-rich system in which CO(2) largely fulfils the role of managing greenhouse gas, and in which methane is necessarily only a trace greenhouse gas, as is N(2)O. Transition from the anoxic to the oxic state risks glaciation. CO(2) build-up during a global snowball may be an essential precursor to a CO(2)-dominated greenhouse with high levels of atmospheric O(2). Photosynthetic and greenhouse-controlling competitions between marine algae, cyanobacteria, and terrestrial C3 and C4 plants may collectively set the CO(2) : O(2) ratio of the modern atmosphere (last few million years ago in a mainly glacial epoch), maximizing the productivity close to rubisco compensation and glacial limits.