Hyperbolic regression analysis for kinetics, electrophoresis, ELISA, RIA, Bradford, Lowry, and other applications

Hyperbolic regression analysis is an effective method for fittingexperimental data points obtained from a variety of experimentsin molecular biology, including enzyme kinetics, agarose gelelectrophoresis of DNA fragments, SDS—polyacrylamide gelelectrophoresis of proteins, enzyme–linked immunosorbentassays (ELISA), radioimmunoassays (RIA), Bradford protein quantitationassays, Lowry protein assays, and other applications. Hyperbolicregression yields excellent fitted curves without the biasesthat are introduced by carrying out linear regression on doublereciprocal coordinates, and it produces one simple equation,encompassing all the data points, that can be used easily ina pocket calculator to estimate the values of unknown samplesfrom the known standards. Received on February 9, 1986; accepted on April 11, 1986     

Structural Organization of Multiple Alphoid Subsets Coexisting on Human Chromosomes 1, 4, 5, 7, 9, 15, 18, and 19

FISH experiments on metaphase chromosomes, interphase nuclei, and extended chromatin were performed to investigate the structural organization of alphoid subsets coexisting on human chromosomes 1, 4, 5, 7, 9, 15, 18, and 19. Results indicate that multiple subsets present on chromosomes 5, 7, 15, 18, and 19 are organized in structurally distinct and contiguous domains, while those on chromosomes 4 and 9 give perfectly overlapping signals. Chromosome 1 shows a peculiar organization: probe pAL1, specific for this chromosome, detects two distinct domains separated by the subset identified by probe pZ5.1. The order along the chromosome of alphoid subsets lying on chromosomes 5, 7, 15, 18, and 19, organized in distinct blocks, has also been established. The relationship between the structural organization of these alphoid sequences and their evolutionary history in great apes is discussed.     

Reference values for the concentrations of As,Cd, Co,Cr, Cu,Fe, I,Hg, Mn,Mo, Ni,Pb, Se,and Zn in selected human tissues and body fluids

This report attempts to formulate reference ranges of elemental concentrations for 15 trace elements in selected human tissues and body fluids. A set of samples consisting of whole blood, blood serum, urine, milk, liver, and hair were chosen and considered for 15 elements of biological significance: As, Cd, Co, Cr, Cu, F, Fe, I, Hg, Mn, Mo, Ni, Pb, Se, and Zn. The results represent wholly or partially data received from 40 countries of the global regions of Africa, Asia, Europe, North, South, and Central America, Australia, and New Zealand. This survey, even if qualitative, has been useful in demonstrating certain trends of trace-element scenarios around the world. It is of course recognized that both diet and environment exert a strong influence on the distribution pattern of several elements, such as As, Cd, Mn, Pb, Se, and Zn. A limited comparison of the available information on soil status of different countries reflected some interesting associations for elements, such as Mn and Zn. Importantly, this study revealed that only a few countries were in a position to identify a reasonable amount of data on samples requested for this project. Regretably, for a number of countries, any dependable data for even such essential elements as Cu, Fe, and Zn were not available. In view of the nutritional importance of many elements, the time is ripe for concerted efforts by intergovernmental agencies to initiate investigations or commission task forces/projects to generate reliable reference data for selected global regions, which sadly lack data of any kind at present.     

Competitive inhibition and selectivity enhancement by Ca in the uptake of inorganic elements (Be, Na, Mg, K, Ca, Sc, Mn, Co, Zn, Se, Rb, Sr, Y, Zr, Ce, Pm, Gd, Hf) by carrot (Daucus carota cv. U.S. harumakigosun)

We investigated the uptake of inorganic elements (Be, Na, Mg, K, Ca, Sc, Mn, Co, Zn, Se, Rb, Sr, Y, Zr, Ce, Pm, Gd, and Hf) and the effect of Ca on their uptake in carrots (Daucus carota cv. U.S. harumakigosun) by the radioactive multitracer technique. The experimental results suggested that Na, Mg, K, and Rb competed for the functional groups outside the cells in roots with Ca but not for the transporter-binding sites on the plasma membrrane of the root cortex cells. In contrast, Y, Ce, Pm, and Gd competed with Ca for the transporters on the plasma membrane. The selectivity, which was defined as the value obtained by dividing the concentration ratio of an elemental pair, K/Na, Rb/Na, Be/Sr, and Mg/Sr, in the presence of 0.2 and 2 ppm Ca by that of the corresponding elemental pair in the absence of Ca in the solution was estimated. The selectivity of K and Rb in roots was increased in the presence of Ca. The selectivity of Be in roots was not affected, whereas the selectivity of Mg was increased by Ca. These observations suggest that the presence of Ca in the uptake solution enhances the selectivity in the uptake of metabolically important elements against unwanted elements.     

Decreased proteolysis caused by protein aggregates, inclusion bodies, plaques, lipofuscin, ceroid, and 'aggresomes' during oxidative stress, aging, and disease

Protein aggregation seems to be a common feature of several neurodegenerative diseases and to some extent of physiological aging. It is not always clear why protein aggregation takes place, but a disturbance in the homeostasis between protein synthesis and protein degradation seems to be important. The result is the accumulation of modified proteins, which tend to form high molecular weight aggregates. Such aggregates are also called inclusion bodies, plaques, lipofuscin, ceroid, or ‘aggresomes’ depending on their location and composition. Such aggregates are not inert metabolic end products, but actively influence the metabolism of cells, in particular proteasomal activity and protein turnover. In this review we focus on the influence of oxidative stress on protein turnover, protein aggregate formation and the various interactions of protein aggregates with the proteasome. Furthermore, the formation and effects of protein aggregates during aging and neurodegeneration will be highlighted.     

Data, 1H-NMR databases, data manipulation, …

Research on all aspects of marine natural products has become increasingly dependent on access to databases of information on bibliography, taxonomy, compound structures, spectroscopic and physical properties data, and biological activities. Convenient access to and effective use of these databases, especially a ¹H NMR database, can lead to a more efficient use of time and effort in (marine) natural product investigations. A survey of the available databases is presented and how appropriate application can markedly reduce the effort required in the process of dereplication.     

Earth, sky, wind, and weather

This paper seeks to understand what it means to live 'in the open'. It begins with an account of experiments that test whether children have acquired a scientifically correct understanding of the shape of the earth, according to which people live all around on the outside of a solid sphere. This understanding cannot accommodate the phenomenon of the sky, in relation to which the earth can appear only as the ground of human habitation. James Gibson's ecological approach to perception offers a possible alternative, depicting earth and sky as complementary hemispheres. Yet for Gibson, this earth-sky can be inhabited only insofar as it is furnished with objects. To that extent, it ceases to be open. Drawing on elements of Merleau-Ponty's phenomenology, it is argued that in the open world persons and things relate not as closed forms but by virtue of their common immersion in the generative fluxes of the medium – in wind and weather. Fundamental to life is the process of respiration, by which organisms continually disrupt any boundary between earth and sky, binding substance and medium together in forging their own growth and movement. Thus to inhabit the open is not to be stranded on the outer surface of the earth but to be caught up in the transformations of the weather-world.     

From Bretonneau to therapeutic antibodies,from specificity to specific remedies,Saint-Cyr-Sur-Loire,France, November 19, 2012

Held on November 19, 2012 in Saint-Cyr-sur-Loire, France, the symposium “From Bretonneau to therapeutic antibodies, from specificity to specific remedies” focused on the historical development of antibodies as therapeutics, with an emphasis on the seminal work of the French physician Pierre-Fidèle Bretonneau (1778–1862). The morning session was devoted to discussion of the evolution of the concept of specificity in medicine, which started with an epistemological definition. The contributions of Bretonneau to the emergence of the concept of specificity, notably with his studies on diphtheria, and the subsequent development of antidiphtheric serotherapy in Europe during the period 1894–1898 were then presented in detail. The afternoon session began with a presentation on the role of French physiologists during the years 1860–1890 in establishing the basic concepts of specific immunity and the principles of serotherapy. The history of antivenom serotherapy, particularly its discovery by Césaire Phisalix, and the development of antilymphocyte globulins as successful transplantation drugs were then discussed. The symposium ended with the inauguration of a stele representing Bretonneau, who lived in Saint-Cyr-sur-Loire and died 150 y ago.     

Cellular polyamines of the acidophilic, thermophilic and thermoacidophilic archaebacteria, Acidilobus, Ferroplasma, Pyrobaculum, Pyrococcus, Staphylothermus, Thermococcus, Thermodiscus and Vulcanisaeta

Cellular polyamines of newly isolated acidophilic, thermophilic and thermoacidophilic archaebacteria were investigated for the chemotaxonomic significance of polyamine distribution profiles. In addition to spermidine, spermine and agmatine, a quaternary branched penta-amine, N(4)-bis(aminopropyl)spermidine, was found in thermophilic Thermococcus waiotapuensis, Thermococcus aegaeus and Pyrococcus glycovorans belonging to the order Thermococcales. An acidophilic euryarchaeon, Ferroplasma acidiphilum located in the order Thermoplasmatales, contained spermidine and agmatine. Norspermidine, spermidine, norspermine and spermine were found in thermoacidophilic Acidilobus aceticus and thermophilic Thermodiscus maritimus located in the order Desulfurococcales, and in thermophilic Pyrobaculum arsenaticum, Pyrobaculum oguniense, Vulcanisaeta distributa and Vulcanisaeta souniana belonging to the order Thermoproteales; however, the four genera differ on their tetra- and penta-amine levels. Thermophilic Staphylothermus hellenicus belonging to Desulfurococcales contained caldopentamine, caldohexamine and N1-acetylcaldopentamine in addition to norspermidine, spermidine and norspermine. This is the first report on the occurrence of acetylated penta-amine in nature.     

Effects of streptomycin,cycloheximide, Fungizone,captan, carbofuran,cygon, and PCNB on soil microorganisms

Eight biocides were chosen to determine whether they had any effects on nontarget organisms in soil and to what extent they would reduce their target populations under laboratory experimental conditions. A simplified microcosm system was utilized in which reduced species arrays that included field populations of either only bacteria and fungi, or bacteria, fungi, and protozoa (no nematodes, arthropods, or plants) were inoculated into sterilized soil. In a second set of experiments, plants were grown in sterilized soil. A bactericide-streptomycin-four fungicides-cycloheximide, Fungizone (amphotericin B), captan, and PCNB (quintozene)-an acaricide-cygon-an insecticide-nematicide-carbofuran-and an insecticide-diazinon-were used. Each biocide had effects on nontarget organisms although the increases or decreases, with respect to the control, were of only limited duration. Reductions in target groups were typically of longer duration. Streptomycin, applied at 1 mg·g^–1 soil, did not decrease bacterial populations during the experimental incubation. At 3 mg·g^–1 soil, streptomycin decreased the numbers of bacteria that grew on tryptone agar, but also reduced active hyphae. Fungizone was the most effective of the 4 fungicides tested in reducing active hyphae. Increased bacterial populations were usually observed following fungal reductions. Carbofuran had the fewest effects on the test organisms (bacteria, fungi, and protozoa). Only an initial stimulation of bacterial and fungal populations was observed with cygon although it also increased NH₄ ⁺-N concentrations in soil during most of the incubation, as did streptomycin and cycloheximide. A transitory increase in fungal populations following a decrease in ciliate numbers was observed in the cygon with grazers treatments. Diazinon reduced all microbial populations and inorganic nitrogen concentrations measured. Cygon and PCNB decreased growth of blue grama plants, while streptomycin reduced shoot weights of blue grama. These results should be useful in assessing the effects of these biocides when applied to more complex systems.     

Mycoplasma contamination of cell cultures: Incidence, sources, effects, detection, elimination, prevention

The contamination of cell cultures by mycoplasmas remains a major problem in cell culture. Mycoplasmas can produce a virtually unlimited variety of effects in the cultures they infect. These organisms are resistant to most antibiotics commonly employed in cell cultures. Here we provide a concise overview of the current knowledge on: (1) the incidence and sources of mycoplasma contamination in cell cultures, the mycoplasma species most commonly detected in cell cultures, and the effects of mycoplasmas on the function and activities of infected cell cultures; (2) the various techniques available for the detection of mycoplasmas with particular emphasis on the most reliable detection methods; (3) the various methods available for the elimination of mycoplasmas highlighting antibiotic treatment; and (4) the recommended procedures and working protocols for the detection, elimination and prevention of mycoplasma contamination. The availability of accurate, sensitive and reliable detection methods and the application of robust and successful elimination methods provide powerful means for overcoming the problem of mycoplasma contamination in cell cultures. This revised version was published online in August 2006 with corrections to the Cover Date.     

Interactions between red-billed oxpeckers, Buphagus erythrorhynchus, and domestic cattle, Bos taurus, in Zimbabwe

Many apparent interspecific mutualisms are poorly understood. Although theory has focused on the various evolutionary problems peculiar to mutualism, especially the need to identify mechanisms that protect a mutualism from cheating or exploitation, there are relatively few quantified examples of how organisms actually interact. Oxpeckers are believed to benefit their mammalian hosts by reducing tick loads, an assumption based on the fact that the birds include ticks in their diet. I watched red-billed oxpeckers foraging on domestic cattle in the Limpopo Valley between August 1996 and September 1997. From focal watches of 41 individually colour-ringed oxpeckers, I found that birds fed mainly on wounds, in ears and by 'scissoring' with the bill (a distinctive feeding technique). Observable tick feeding represented a very small percentage of their foraging time. Based on oxpecker behaviour at feeding sites, blood from open wounds appeared to be the favoured food: oxpeckers displaced each other significantly more, and were significantly less likely to be deterred by the cows' attempts to remove them, when feeding on a wound than at other feeding sites. The preference for blood, the inability of cows to prevent oxpeckers feeding on blood and the relatively small amount of visible tick feeding suggest that, certainly for cattle, oxpeckers may not be beneficial. However, as cows have not coevolved with oxpeckers, these results may not be representative of oxpecker relations with native African mammalian hosts. Copyright 1999 The Association for the Study of Animal Behaviour.     

Bacteriocins: criteria,classification, characteristics,methods of detection

The review on bacteriocins of Gram negative and Gram positive bacteria. Criteria making it possible to regard antagonistic substances as bateriocins or bacteriocin-like substances and on their classification are presented. Examples of bacteriocins naming depending on the taxonomic position of the producer culture are given. Information on the physico-chemical and biological properties of bacteriocins and their purification is presented as well as on detection tools of bacteriocins in microorganisms and evaluation of the producer activity of the bacteriological culture.     

Lipid,lipoprotein, and apolipoprotein models: past,present, and future

Mones Berman's untimely death on 12 August 1982 put an end to his work in the development of theoretical biology. Arguments are examined, and it is concluded that a formal theory of lipoprotein metabolism flourished and expanded under the guidance of Dr. Berman. Not many scientists in the field of biology spend a major portion of their energies on theoretical work xxx was outstanding because of his early decision to follow the theoretical path.     

Potential Compounds for Oral Cancer Treatment: Resveratrol,Nimbolide, Lovastatin,Bortezomib, Vorinostat,Berberine, Pterostilbene,Deguelin, Andrographolide,and Colchicine

Oral cancer is one of the main causes of cancer-related deaths in South-Asian countries. There are very limited treatment options available for oral cancer. Research endeavors focused on discovery and development of novel therapies for oral cancer, is necessary to control the ever rising oral cancer related mortalities. We mined the large pool of compounds from the publicly available compound databases, to identify potential therapeutic compounds for oral cancer. Over 84 million compounds were screened for the possible anti-cancer activity by custom build SVM classifier. The molecular targets of the predicted anti-cancer compounds were mined from reliable sources like experimental bioassays studies associated with the compound, and from protein-compound interaction databases. Therapeutic compounds from DrugBank, and a list of natural anti-cancer compounds derived from literature mining of published studies, were used for building partial least squares regression model. The regression model thus built, was used for the estimation of oral cancer specific weights based on the molecular targets. These weights were used to compute scores for screening the predicted anti-cancer compounds for their potential to treat oral cancer. The list of potential compounds was annotated with corresponding physicochemical properties, cancer specific bioactivity evidences, and literature evidences. In all, 288 compounds with the potential to treat oral cancer were identified in the current study. The majority of the compounds in this list are natural products, which are well-tolerated and have minimal side-effects compared to the synthetic counterparts. Some of the potential therapeutic compounds identified in the current study are resveratrol, nimbolide, lovastatin, bortezomib, vorinostat, berberine, pterostilbene, deguelin, andrographolide, and colchicine.     

Count data, detection probabilities, and the demography, dynamics, distribution, and decline of amphibians

The evidence for amphibian population declines is based on count data that were not adjusted for detection probabilities. Such data are not reliable even when collected using standard methods. The formula C = Np (where C is a count, N the true parameter value, and p is a detection probability) relates count data to demography, population size, or distributions. With unadjusted count data, one assumes a linear relationship between C and N and that p is constant. These assumptions are unlikely to be met in studies of amphibian populations. Amphibian population data should be based on methods that account for detection probabilities.     

In vivo effects of ELF MFs on collagen synthesis, free radical processes, natural antioxidant system, respiratory burst system, immune system activities, and electrolytes in the skin, plasma, spleen, lung, kidney, and brain tissues

In this study, the results related with the effects of 50 Hz, 0.2 mT-3 mT MFs exposures on collagen synthesis, epilepsy, electrolytes, lipid peroxidation (MDA), Nitric Oxide (NOx), respiratory burst system (MPO), antioxidant defense system (GSH), and immune system (NK cell activity) in spleen, skin, lung, kidney, brain, and plasma tissues performed at Gazi Biophysics Department are reviewed. Our studies indicate that ELF MFs had effects on the tissues examined.     

Penetration,Development, and Reproduction of Heterodera schachtii on Fagopyrum esculentum,Phacelia tanacetifolia,Raphanus sativus,Sinapis alba,and Brassica oleracea

The penetration, development, and reproduction of a California population of the sugarbeet cyst nematode, Heterodera schachtii, was observed on cultivars of cabbage (Brassica oleracea), phacelia (Phacelia tanacetifolia), buckwheat (Fagopyrum esculentum), oilseed radish (Raphanus sativus), and white mustard (Sinapis alba). With the exception of the nonhost, phacelia, all were readily penetrated by second-stage juveniles of H. schachtii. After 38 days at 25 C, no cysts were observed on phacelia cv. Angelia or on the oilseed radish cv. Nemex and Pegletta. Cyst production was low (<2.5 cysts/plant) on the buckwheat cv. Tardo and Prego and most of the oilseed radish cultivars. Cyst production was intermediate (5-14 cysts/plant) on most of the white mustard cultivars, and high on cabbage (20-110 cysts/plant). In microplot studies conducted over 133 days (approx. 450 degree-days, base 8 C), the reproductive index for H. schachtii was greater than 1.0 for cultivars of phacelia, oilseed radish, and white mustard as welt as in fallow treatments, indicating the need for further research on the use of these crops under field conditions.     

Marine pharmacology in 2001--2002: marine compounds with anthelmintic, antibacterial, anticoagulant, antidiabetic, antifungal, anti-inflammatory, antimalarial, antiplatelet, antiprotozoal, antituberculosis, and antiviral activities; affecting the cardiovascular, immune and nervous systems and other miscellaneous mechanisms of action

During 2001--2002, research on the pharmacology of marine chemicals continued to be global in nature involving investigators from Argentina, Australia, Brazil, Canada, China, Denmark, France, Germany, India, Indonesia, Israel, Italy, Japan, Mexico, Netherlands, New Zealand, Pakistan, the Philippines, Russia, Singapore, Slovenia, South Africa, South Korea, Spain, Sweden, Switzerland, Thailand, United Kingdom, and the United States. This current article, a sequel to the authors' 1998, 1999 and 2000 marine pharmacology reviews, classifies 106 marine chemicals derived from a diverse group of marine animals, algae, fungi and bacteria, on the basis of peer-reviewed preclinical pharmacology. Anthelmintic, antibacterial, anticoagulant, antifungal, antimalarial, antiplatelet, antiprotozoal, antituberculosis or antiviral activities were reported for 56 marine chemicals. An additional 19 marine compounds were shown to have significant effects on the cardiovascular, immune and nervous system as well as to possess anti-inflammatory and antidiabetic effects. Finally, 31 marine compounds were reported to act on a variety of molecular targets and thus may potentially contribute to several pharmacological classes. Thus, during 2001--2002 pharmacological research with marine chemicals continued to contribute potentially novel chemical leads for the ongoing global search for therapeutic agents for the treatment of multiple disease categories.     

Plastid stromules: video microscopy of their outgrowth, retraction, tensioning, anchoring, branching, bridging, and tip-shedding

Summary. Stromules are stroma-containing tubules which can grow from the surface of plastids, most commonly leucoplasts and chromoplasts, but also chloroplasts in some tissues. Their functions are obscure. Stills from video rate movies are presented here. They illustrate interaction of stromules with cytoskeletal strands and the anchoring of stromules to unidentified components at the cell surface. Anchoring leads to stretching and relaxation of stromules when forces arising from cytoplasmic streaming act on the attached, freely suspended plastid bodies. Data on stromule growth, retraction, and regrowth rates are provided. Formation and movement of stromular branches and bridges between plastids are described. The shedding of a tip region into the streaming cytoplasm is recorded in frame-by-frame detail, in accord with early observations. Correspondence and reprints: Plant Cell Biology Group, Research School of Biological Sciences, Australian National University, PO Box 475, Canberra, ACT 2601, Australia.