Galactic Factors,the Young Sun,the Earth,and the Biophysics of Living Systems

The effects of radiation from the young Sun and galactic cosmic rays on the physical conditions on the early Earth are significantly underestimated in studies of the problems related to the origin and evolution of the biosphere. This review considers the dynamics of solar and galactic processes over the 4.56 billion years of the existence of the Solar System. These factors substantially affected the development of adaptive technologies in ancient and modern living systems. The features of biosphere development are considered for the early Earth under the young Sun, which was fainter, but more flare active. The radiation spectrum of the young Sun is discussed together with the paradoxical mismatch between the solar radiation spectrum and the chlorophyll adsorption spectrum. Ways of solving the paradox are proposed. The role of solar radiation is important when studying models of the early biosphere of the Earth and hypothetical biospheres of giant planet satellites and exoplanets.

     

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.     

Formation of pyrophosphate,tripolyphosphate, and phosphorylimidazole with the thioester,N, S-diacetylcysteamine,as the condensing agent

Summary Reaction of 0.20M orthophosphate with 0.20M N,S-diacetylcysteamine in 0.40M imidazole at pH 7.0 or 8.0 under drying conditions at 50°C for 6 days yields pyrophosphate and tripolyphosphate in the presence and absence of 0.10M divalent metal ion. The efficiency of utilization of N,S-diacetylcysteamine in the formation of pyrophosphate linkages ranges from 3 – 8% under the above conditions. The thioester, N,S-diacetylcysteamine, and imidazole are required for phosphoanhydride formation.Reaction of 0.40M orthophosphate with 0.20M N, S-diacetylcysteamine in 0.40M imidazole at ambient temperature for 6 days yields phosphorylimidazole in the absence or presence of 0.05M MgCl₂. Phosphorylimidazole and pyrophosphate are formed in the presence of 0.05M CaCl₂; pyrophosphate and tripolyphosphate are formed with 0.15M CaCl₂. The efficiency of utilization of N,S-diacetylcysteamine in the formation of pyrophosphate linkages is roughly 7% at 6 days of reaction with 0.15M CaCl₂. The thioester, N,S-diacetylcysteamine and imidazole are required for the formation of phosphoanhydrides. The significance of these reactions to molecular evolution is discussed.Abbreviations P₁ orthophosphate - P₂ pyrophosphate - P₃ tripolyphosphate - ImP phosphorylimidazole - Ac-Csa(Ac) N, S-diacetylcysteamine - Im imidazole     

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.     

Arsenic Concentrations in the Surface,Well, and Drinking Waters of the Hisarcik,Turkey, Area

Arsenic is one of the most important water pollutants because of its carcinogenicity. The association between arsenical poisoning and the development of internal malignancies and skin cancer is well known. The U.S. Environmental Protection Agency (USEPA) sets maximum contaminant level goals at zero for carcinogens. In this study are presented groundwater arsenic concentrations in the area of naturally rich boron sources of Turkey. Water samples were collected from the Hisarcik, Turkey, area, which has a large boron mine. An inductively coupled plasma/mass spectrometry method was used to analyze arsenic concentrations in water samples. The arsenic levels in water ranged from no detectable amounts to 3.00 mg As/L (mean: 0.46 ± 0.07SD). This mean As level exceeds by a factor of 10 the USEPA's current Maximum Contaminant Level of 0.05 mgAs/L. Some possible health problems associated with consumption of arsenic-contaminated water are discussed and public health interventions proposed.     

Ethology, Natural History, the Life Sciences, and the Problem of Place

Investigators of animal behavior since the eighteenth century have sought to make their work integral to the enterprises of natural history and/or the life sciences. In their efforts to do so, they have frequently based their claims of authority on the advantages offered by the special places where they have conducted their research. The zoo, the laboratory, and the field have been major settings for animal behavior studies. The issue of the relative advantages of these different sites has been a persistent one in the history of animal behavior studies up to and including the work of the ethologists of the twentieth century. This revised version was published online in July 2006 with corrections to the Cover Date.     

Health-risk assessment related to the fluoride,nitrate, and nitrite in the drinking water in the Sanandaj,Kurdistan County,Iran

The concentration of fluoride and nitrate in groundwater is usually higher than that of surface water. The main objective of this study was to estimate the health-risk assessment associated with fluoride, nitrate, and nitrite in drinking water in Sanandaj and its villages. The number of samples in the Sanandaj and its rural was 106. The average concentration of fluoride in urban and rural drinking water was 0.22 mg/l and 0.27 mg/l, respectively. Fluoride concentration was also close to urban and rural drinking water. The concentration of nitrate in urban and rural drinking water was in the range between 0.28–27.77 mg/l and 1.28–80 mg/l, respectively. The concentration of nitrate reported in rural samples was higher than that of urban samples. The maximum concentration of nitrate reported in this study was 80 mg/l. The mean CDI for nitrate in the men, women, and children was 0.4258, 0.5110, and 1.1454, respectively. The findings of this study indicated that all three groups studied were exposed to nitrate contact hazards (HQ > 1). Therefore, the HQ in each of the three groups was higher than 1, which should be carefully monitored and necessary measures should be performed.     

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.     

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.     

Age and growth of the ajime-loach,niwaella delicata, in the yura river, kyoto, japan

The age of the Ajime-loach,Niwaella delicata (a species endemic to Japan), was determined from the number of concentric rings appearing on the cross-sectional surface of the erectile spine (peculiar to Cobitidae). The ages of loaches caught in the Yura River, Kyoto, were determined and growth rates for each sex estimated. It was found that size dimorphism in this species was due to different growth patterns between the sexes, 2.5 years old males being larger than females and usually sexually mature, unlike the latter. Females older than 3.5 years were sexually mature and larger than males of equivalent age.     

Galactosemia: the good, the bad, and the unknown

Alpha-D-galactose is metabolized in species ranging from E. coli to mammals predominantly via a series of sequential reactions collectively known as the Leloir pathway. Deficiency of any one of these enzymes in humans results in a form of the inherited metabolic disorder, galactosemia, although the symptoms and severity depend upon the enzyme impaired, and the degree of functional deficiency (Tyfield and Walter, 2002, The Metabolic and Molecular Bases of Inherited Disease. New York: McGraw Hill.). Studies of these enzymes, and the disorders associated with their loss, have led to a much deeper appreciation of the intricate and interwoven levels of regulation that govern their normal function. These insights have further identified likely mediators of outcome severity in patients, and have enabled a rational approach to the development of novel strategies of intervention.     

Sir2 and the acetyltransferase, Pat, regulate the archaeal chromatin protein, Alba

The DNA binding affinity of Alba, a chromatin protein of the archaeon Sulfolobus solfataricus P2, is regulated by acetylation of lysine 16. Here we identify an acetyltransferase that specifically acetylates Alba on this residue. The effect of acetylation is to lower the affinity of Alba for DNA. Remarkably, the acetyltransferase is conserved not only in archaea but also in bacteria where it appears to play a role in metabolic regulation. Therefore, our data suggest that S. solfataricus has co-opted this bacterial regulatory system to generate a rudimentary form of chromatin regulation.     

Mitosis, microtubules, and the matrix

The mechanical events of mitosis depend on the action of microtubules and mitotic motors, but whether these spindle components act alone or in concert with a spindle matrix is an important question.     

Population ecology of the ring-tailed lemur, Lemur catta, and the white sifaka, Propithecus verreauxi verreauxi, at Berenty, Madagascar, 1981

The diurnal lemurs Propithecus verreauxi verreauxi and Lemur catta at Berenty in southern Madagascar, have been studied for the last 30 years. The August 1981 census indicates that the population size of L. catta remains stable at 150 adults but that P. v. verreauxi troops have become fragmented and scattered and the population is apparently increasing. Eight different vegetation types were classified within the reserve and their influence on the distribution of L. catta and P. v. verreauxi investigated. Behavioural data obtained shows the niche separation between these two, potentially competitive, sympatric lemurs.     

Nile perch,Lates niloticus,predation on the freshwater prawn,Caridina nilotica,in the Nyanza Gulf,Lake Victoria,East Africa

Synopsis The percentage of Nile perch, Lates niloticus, containing the prawn, Caridina nilotica, declined from 60–85%, for fish between 5 and 40 cm total length, to less than 10% for fish larger than 80 cm in length. The maximum number of prawns eaten by a Nile perch increased steadily, from 10 prawns for a fish in the 5–9.9 cm length group, to 913 prawns in a fish in the 60–69.9 cm length group, and then fell sharply for larger fish. The mean number of Caridina eaten by fish that were foraging on this animal followed a similar trend. Gill raker spacing increased in direct proportion to fish length and this may prevent fish larger than 70 cm in length from being effective prawn predators.     

Parasitism of the deer ked,Lipoptena cervi,on the moose,Alces alces,in eastern Finland

The deer ked, Lipoptena cervi L. (Diptera: Hippoboscidae), is an ectoparasitic fly that spread to Finland in the early 1960s from the southeast across the Soviet border. It is currently a common parasite of the moose, Alces alces (Artiodactyla: Cervidae), in the southern part of the country and its area of distribution is gradually spreading to Finnish Lapland, where it will come into contact with another potential cervid host, the semi‐domesticated reindeer, Rangifer tarandus tarandus. The aim of this study was to determine the intensity of deer ked parasitism on the moose in eastern Finland. Whole skins of 23 moose were examined for the presence of deer keds, which were extracted and their total numbers estimated. The intensity of deer ked parasitism was correlated to the age, sex, skin area and anatomical region of the host. Bulls had the highest total number of keds (10616 ± 1375) and the highest deer ked density (35.7 ± 4.4 keds/dm² of skin). Cows had a higher total number of keds than calves (3549 ± 587 vs. 1730 ± 191), but ked densities on cows and calves were roughly equal (11.8 ± 1.7 vs. 9.4 ± 1.1 keds/dm² of skin). The density of keds was highest on the anterior back, followed by the posterior back, front limbs, abdomen, head and hind limbs. The sex ratio of deer keds was close to equal (male : female, 1.0 : 1.1). After they had consumed blood, male keds were heavier than females. As the total numbers and densities of deer keds were higher than reported previously on moose or for any other louse fly species, the effects of parasitism on the health of the host species should be determined.     

Llandovery sporomorphs and graptolites from the Manbo Formation,the Mojiang County,Yunnan, China

Llandovery sporomorphs and graptolites have been recovered from the Manbo Formation, Mojiang area, western Yunnan, China, which belonged to the Indo-China Palaeoplate in the Palaeozoic. The graptolite fauna, including 8 genera and 12 species, is considered Mid Telychian, Llandovery in geological age, confirming the existence of Llandovery rocks in this region. The Silurian stratigraphical sequence of this area is reconsidered as in the ascending order: Manbo Formation (Llandovery–early Wenlock), Shuiqing Formation (late Wenlock–Ludlow) and unnamed formation (Pridoli?). The sporomorph assemblage from the Manbo Formation includes seven species in five genera. The dominant members of this assemblage are Tetrahedraletes medinensis and Laevolancis chibrikovae. Based on the low diversity and low abundance, the geological age of this assemblage is considered to be approximately the Telychian, Llandovery. The parent plants of sporomorphs probably inhabited the landmass near Mojiang area, these sporomorph-producing plants probably included bryophyte-like land plants and primitive vascular land plants. The sporomorph evidence shows that the South China and Indo-China palaeoplates may have been in close proximity (maybe with some continental bridges linking them) to each other at least in the Llandovery. They were also closely related with Gondwanaland in the Llandovery.     

Speciation,phenotypic plasticity,or ontogeny,the case of the genus Galkinius (Pyrgomatidae,Cirripedia, Crustacea)

Barnacles of the genus Galkinius occupy a large spectrum of host corals, making it one of the least host‐specific genera within the Pyrgomatidae. Molecular analyses show that within the genus Galkinius there are highly supported clades, suggesting that the genus Galkinius is a complex of evolutionarily significant units (ESUs). The morphology of the opercular valves has been used as the basis for the separation of species of Galkinius. In this study, morphological variability was found both between specimens within ESUs extracted from different host species and between specimens extracted from the same colony. Identifications based on the opercular valves cannot therefore be assigned to different species despite being genetically distinguishable. It is proposed that in many cases the differences between valve morphology of different species of Galkinius are the outcome of ontogeny. Allometric growth of the valves has resulted in differences in the proportions of the parts of the valve. © 2015 The Linnean Society of London     

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.