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.     

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.     

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.     

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.     

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.     

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.     

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.     

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.     

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.     

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.     

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.     

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.     

Sympathetic Activity,Age, Sucrose Preference,and Diet-Induced Obesity

Only half the adult male Sprague-Dawley rats which are placed on a diet relatively high in calories, fat, and sucrose (HE diet) develop diet-induced obesity (DIO). The rest are diet-resistant (DR). Some chowfed rats prone to develop DIO on an HE diet have greater initial food intake of this diet and all have greater glucose-induced plasma norepinephrine (NE) increases than DR-prone rats. Here we looked for a relationship of sucrose preference or 24-hour urinary catecholamine excretion as possible phenotypic markers of the DIO- and DR-prone states before HE diet exposure as a function of age. When begun on an HE diet at 3 months of age, DIO-prone rats gained 30% more weight over 3 months than DR-prone rats and had 35% heavier retroperitoneal fat pads. While still on chow, sucrose preferences were similar, but 24 hour urine NE levels were 29% higher in DIO-than in DR-prone rats. The slope of the curve of urine NE versus body weight gain after 3 months on HE diet was 4-fold greater in DIO- thaain DR-prone rats. After 3 months on the HE diet, there was no statistical relationship between 24-hour urine NE and body weight or prior body weight gain in DIO or DR rats. Six-month-old DIO-prone rats had 126% and 128% more urine NE and gained 112% and 232% more weight after 3 months on HE diet than DR-prone and chowfed rats, respectively. Only DIO-prone rats showed a correlation (r=0.879; p=O.OS) between urine NE levels and subsequent weight gain on HE diet. Thus, 3- or 6- month-old DIO- and DR-prone rats can be identified by their 24-hour basal urine NE levels but not sucrose preference prior to HE diet exposure. While this may suggest higher basal sympathetic activity in DIO-prone rats, other explanations are possible. (OBESITY RESEARCH 1993;1:281–287)     

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.     

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.     

Cadmium transport, resistance, and toxicity in bacteria, algae, and fungi

Cadmium is an important environmental pollutant and a potent toxicant to bacteria, algae, and fungi. Mechanisms of Cd toxicity and resistance are variable, depending on the organism. It is very clear that the form of the metal and the environment it is studied in, play an important role in how Cd exerts its effect and how the organism(s) responds. A wide range of Cd concentrations have been used to designate resistance in organisms. To date, no concentration has been specified that is applicable to all species studied under standardized conditions. Cadmium exerts its toxic effect(s) over a wide range of concentrations. In most cases, algae and cyanobacteria are the most sensitive organisms, whereas bacteria and fungi appear to be more resistant. In some bacteria, plasmid-encoded resistance can lead to reduced Cd2+ uptake. However, some Gram-negative bacteria without plasmids are just as resistant to Cd as are bacteria containing plasmids encoding for Cd resistance. According to Silver and Misra (1984), there is no evidence for enzymatic or chemical transformations associated with Cd resistance. Insufficient information is available on the genetics of Cd uptake and resistance in cyanobacteria and algae. Mechanisms remain largely unknown at this point in time. Cadmium is toxic to these organisms, causing severe inhibition of such physiological processes as growth, photosynthesis, and nitrogen fixation at concentrations less than 2 ppm, and often in the ppb range (Tables 2 and 3). Cadmium also causes pronounced morphological aberrations in these organisms, which are probably related to deleterious effects on cell division. This may be direct or indirect, as a result of Cd effects on protein synthesis and cellular organelles such as mitochondria and chloroplasts. Cadmium is accumulated internally in algae (Table 4) as a result of a two-phase uptake process. The first phase involves a rapid physicochemical adsorption of Cd onto cell wall binding sites, which are probably proteins and (or) polysaccharides. This is followed by a lag period and then a slow, steady intracellular uptake. This latter phase is energy dependent and may involve transport systems used to accumulate other divalent cations, such as Mn2+ and Ca2+. Some data indicate that Cd resistance, and possibly uptake, in algae and cyanobacteria is controlled by a plasmid-encoded gene(s). Although considerable information is available on Cd toxicity to, and uptake in fungi, further work is clearly needed in several areas. There is little information about Cd uptake by filamentous fungi, and even in yeasts, information on the specificity, kinetics, and mechanisms of Cd uptake is limited.(ABSTRACT TRUNCATED AT 400 WORDS)