How does radiation damage in protein crystals depend on X-ray dose?

Is radiation damage to cryopreserved protein crystals strictly proportional to accumulated dose at the high-flux density of beams from undulators at third-generation synchrotron sources? The answer is "yes," for overall damage to several different kinds of protein crystals at flux densities up to 10(15) ph/sec/mm(2) (APS beamline 19-ID). We find that, at 12 keV (1 A wavelength), about ten absorbed photons are sufficient to "kill" a unit cell. As this corresponds to about one elastically scattered photon, each unit cell can contribute only about one photon to total Bragg diffraction. The smallest crystal that can yield a full data set to 3.5 A resolution has a diameter of about 20 microm (100 A unit cell).     

Eine Interferenzfilter-Monochromatoranlage für photobiologische Zwecke

Summary A recently designed interference-filte monochromator system for biological purposes is described (spectral range: 400–800 m). The system contains 6 monochromator units. It operates with projection lamps (500 or 750 W) as sources of radiation. In each unit the optical system of a high-power projector (Prado 500, Leitz) is used. The irradiances which can be obtained with a single interference-filter are rather high: about 1500 ergs/cm². sec at 412 m, about 14000 ergs/cm². sec at 613 m. — In addition to the monochromator system the designs of standard-fields of radiation for red and far-red are presented and data are given concerning a sensitive thermopile Multiflex-galvanometer system. The design is compared in principle with the spectrograph (introduction) and more in detail with the interference-filter monochromator system presented byWithrow (1957).Mit 9 Textabbildungen     

Structural Features of Pregna-D′-pentaranes Determining Their Interaction with Three Rat Proteins

Competition of a number of progesterone 16,17-cycloalkane derivatives with ³H-labeled ligands for the binding sites of rat uterine progesterone receptor, uterine pentaranophilin, and blood serum pentaranophilin was studied. We found that the selective ligands for the progesterone receptor are progesterone, 16,17-cyclopropanoprogesterone, and 16,17-cyclopent-3-enoprogesterone and the selective ligands for serum pentaranophilin are 6-methyl-16,17-cyclohexanopregna-1,4-diene-3,20-dione and 3-hydroxy-16,17-cyclohexanopregn-5-en-20-one. No selective ligands for the uterine pentaranophilin were found. The majority of substituents in rings A, B, and D we studied decreased the affinity of ligands for all the three proteins. The substitution of the ⁵-3-hydroxy grouping for the ⁴-3-keto grouping exerted the strongest negative effect in the case of the progesterone receptor and the uterine pentaranophilin, whereas the introduction of the 3,4-dimethyl grouping strongly inhibited the ligand affinity for the uterine pentaranophilin. The extent and even the direction of the effect of a substituent on the affinity of ligands for the proteins substantially depended on the presence of other substituents in the steroid molecules. We hypothesized that a certain similarity exists between three proteins studied in respect to the structures of their ligand-binding pockets.     

Dream Bizarreness and Inner Thought

The paper offers a critique of bizarreness studies that compare dreams to real world probability ratios and directed thought processes as a basis for determining the degree of bizarreness in dreams. It examines two cases from the literature and suggests that dreams are better compared to non-directed, or imaginative waking thought processes, specifically Inner Thought and Speech (or speech for oneself, in Lev Vygotsky's definition), in which associative mechanisms operate freely hand in hand with (primarily) visual imagery before logical thought mechanisms come into play. The article suggests that dreams create a world order, or umwelt, with its own distinct cognitive domain in which waking considerations of efficiency, logic, and common sense are only thematically relevant. Dreams follow their own logic and can only be approached as thought-in-progress, or a search for coherence leading up many blind alleys. Finally, the relevance to dreams of the Inner Thought principle of predication, or abbreviation is examined.     

Microbial metabolism of alkylbenzene sulphonates the oxidation of key aromatic compounds by a Bacillus

A Bacillus species originally elected for growth at the expense of alkylbenzene sulphonate detergents was found to metabolise a wide range of aromatic compounds. p-Hydroxybenzoate (PHB) was initially hydroxylated to protocatechuate (PCA) i.e. 3,4-dihydroxybenzoate, which was oxidatively cleaved to succinate and acetyl-CoA by a classical ortho cleavage pathway initiated by a substrate-specific 3, 4-oxygenase: no evidence of an alternative meta cleavage pathway was detected. Several key enzymes of this ortho cleavage pathway were induced by growth of the Bacillus on either PHB or PCA. Both PHB and PCA were able to act as sole source of carbon for energy and overall growth of the microorganism.In strict contrast, the higher homologue p-hydroxyphenylacetate (PHPA), after initial hydroxylation to 3, 4-dihydroxyphenylacetate (DHPA), was oxidatively cleaved to 4-carboxymethyl-2-hydroxymuconic semialdehyde (CMHMS) by a meta cleavage catalysed by a substrate-specific 2, 3-oxygenase: no evidence of an alternative ortho cleavage was detected. Several lines of evidence suggested that CMHMS was not further metabolised by the Bacillus and accumulated in the growth medium. Both PHPA and DHPA were unable to act as sole source of carbon for energy and overall growth.The implication of the occurrence in a single bacterium of two separate oxidative pathways catalysing the cleavage of different aromatic nuclei have been discussed.     

Inheritance of resistance to potato viruses Y and A in progeny obtained from potato cultivars containing gene Ry:evidence for a new gene for extreme resistance to PVA

Extreme resistance in cultivated potato (Solanum tuberosum) to potato viruses Y and A (PVY and PVA) conditioned by the presence of Ry genes introduced from Solanum stoloniferum was described by Cockerham (1970). Cockerham detailed a number of genes which controlled a variety of reactions, including extreme resistance to both viruses (i.e. little or no visible reaction of plants and no viral replication following graft and manual inoculation) controlled by gene Ry _sto. In the present study, cvs Pirola and Barbara, which contain a Ry gene, were found to have extreme resistance to PVY isolates from the ordinary (PVY°), veinal necrosis (PVY^N) and potato tuber necrotic ringspot (PVY^NTN) subgroups, and PVA. The inheritance of this phenotype was examined in seedling progenies obtained by crossing Barbara and Pirola with susceptible cultivars. Segregation data for resistance to PVY and PVA in a progeny involving cv Pirola best fitted a genetical model of one gene controlling extreme resistance to both PVY and PVA, although the possibility that there are two genes, each controlling resistance to one virus but closely linked, cannot be excluded. Segregation data from progenies involving cv Barbara best fitted a genetical model in which there are two independent genes, one controlling extreme resistance to PVA and PVY and a second gene controlling extreme resistance to PVA but not to PVY. This previously unrecognised gene conferring extreme resistance to PVA only, should be given the notation Ra in keeping with nomenclature used for other resistance genes.     

Molecular cloning and heterologous expression in E. coli of cytochrome P45017alpha. Comparison of structural and functional properties of substrate-specific cytochromes P450 from different species

To elucidate the nature of substrate specificity and intrinsic mechanism of hydroxylation of steroids, in the present work we carried out molecular cloning and heterologous expression of cDNA for three new forms of cytochrome P45017 from species of the Bovidae family (sheep, goat, and bison), which catalyze 17-hydroxylation of both progesterone (P4) or pregnenolone (P5) and 17,20-lyase reaction resulting in cleavage of side chain with formation of C₁₉-steroids. Recombinant cytochromes P45017 were expressed in E. coli as derivatives, containing a six-His tag at the C-terminal sequence that simplifies purification of the cloned heme proteins using metal-affinity chromatography. Highly purified cytochromes P45017 were used for determination of enzyme activity and specificity in relation to progesterone, pregnenolone, 17-hydroxyprogesterone, and 17-hydroxypregnenolone with registration of the kinetics of reaction product formation using HPLC. It is shown that each form of cytochrome P45017 is characterized by a specific profile of enzyme activity and dependence of 17,20-lyase reaction on the presence of cytochrome b5 in the reaction mixture. The analysis of the activity of the known forms of cytochrome P45017 in view of the data obtained in the present work allows the division of known cytochromes P45017 into three main group: group A (pig, hamster, rat), cytochromes P45017 catalyze the reaction of 17-hydroxylation of both P4 and P5 steroids and the 17,20-lyase reaction of 17-hydroxyprogesterone and 17-hydroxypregnenolone; group B (human, bovine, sheep, goat, and bison), cytochromes P45017, which have no or have insignificant 17,20-lyase activity in relation to 17-hydroxyprogesterone; group C (guinea pig), cytochrome P45017 which either has no or has insignificant 17,20-lyase activity on transformation 17-hydroxypregnenolone to dehydroepiandrosterone.     

Photosynthetic glow peaks and their relationship with the free energy changes

This paper is concerned with relating thermoluminescence to the total free-energy change, G, involved in detrapping a particular electron-hole pair as a photosynthetic sample is warmed from an initial low temperature. It extends a mathematical discussion of four possible mechanisms introduced in an earlier paper [DeVault, Govindjee and Arnold, Proc Nat'l Acad Sci USA 80: 983–987 (1983)]; here, particular attention is paid to the dependence of the absolute temperature of the maximum of a glow-peak, T _m , on the total free-energy change, G. The conclusion from the cases studied is that T _m =G/(k _B W) where G is evaluated at T _m , W is a complicated function of temperature and of thermodynamic parameters in the steps of the mechanism, and k _B is the Boltzmann constant. If the rate limiting step in the mechanism of detrapping is not preceded by any step in which G is appreciably negative, W is likely to have a value of about 33 and T _m is approximately proportional to G. Otherwise W can become much smaller and more strongly dependent on temperature and T _m is no longer proportional to G. These conclusions are of significance in lending theoretical support to the practice of inferring redox midpoint potential changes from shifts in T _m .     

Growth and reproduction as a function of temperature and salinity inClava multicornis (Cnidaria,Hydrozoa)

Summary 1. Rates of growth (length increase of stolons) and of asexual reproduction (increase in number of polyps) were determined in secondaryClava multicornis colonies of a clone exposed to 12 different combinations of water temperature and salinity (12°, 17°, 22° C; 16 , 24 , 32 , 40 S). Sexual reproduction (via gonophores) has been observed only at 12° and 17° C; temperature and salinity ranges are narrower for sexual than for asexual reproduction.2. The data obtained are insufficient for a detailed analysis; they provide, however, interesting insights into the variability of growth and reproduction ofC. multicornis caused by different intensities of temperature and salinity.3. It appears that temperature requirements for maximum colony increase are reduced as the colony grows older.4. One feeding period per 24 hours seems insufficient for maximum growth and reproduction at the higher temperature levels, especially at 22° C.5. The different degrees of environmental stress endured during the initial period of transfer into the test combinations of temperature and salinity have affected the resulting colony size at least up to an age of 39 days. More appropriate criteria for assessment of rates of growth and reproduction are therefore the doubling times (number of days within which stolon length and polyp numbers taken 20 days after initiation of experiments have doubled).6. On the basis of doubling time values, increase in stolon length is progressively reduced with increasing water temperature (12°, 17°, 22° C). At 12° and 17° C stolons grow fastest in 32 , followed by 24 , 16 and 40 S; at 22° C stolon growth rates are identical in 32 and 24 S.7. Doubling times of polyp numbers per colony show a less obvious trend. In 56-day-old colonies, however, stolon length and polyp number are modified to similar degrees by the various temperatures and salinities offered. The sequence of temperatures causing fastest increase in polyp number is 12°>17°>22° C; the respective sequence of salinities reads: 24 , 32 , 16 , 40 S.8. Stolon length and polyp number per colony increase exponentially; most curves obtained exhibit undulations indicating endogenous growth rhythms.9. During the initial period of transfer into the final test media, asexual reproduction via budding seems to have been stimulated by a reduction in salinity.10. The doubling times obtained forC. multicornis are considerably longer than those found forCordylophora caspia and indicate that our culture conditions may have been suboptimal.

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Wachstum und Reproduktion als Funktion von Temperatur und Salzgehalt beiClava multicornis (Cnidaria, Hydrozoa)

Kurzfassung Einzelpolypen eines Klons vonC. multicornis Forskål wurden schrittweise in 12 verschiedene Temperatur-Salzgehalts-Kombinationen überführt und — während sie zu neuen Kolonien heranwuchsen — das Längenwachstum ihrer Stolonen, die Geschwindigkeit ihrer asexuellen Vermehrung durch Knospung neuer Hydranthen sowie die Gonophorenausbildung (sexuelle Fortpflanzung) registriert. Die erhaltenen Daten sind unzureichend für eine detaillierte Analyse, gewähren jedoch interessante Einblicke in die Bedeutung der verschiedenen Temperatur- und Salzgehaltsbedingungen für Wachstum und Vermehrung. Die anfängliche, schrittweise Überführung in die Testmedien verursacht per se Leistungsunterschiede, deren Auswirkungen sich mindestens bis zu einem Alter von 39 Tagen verfolgen lassen. Doubling times stellen daher objektivere Kriterien dar als absolute Zuwachswerte. Die doubling times von Kolonien, welche länger als 20 Tage in den Testmedien gewachsen waren, zeigen eine Verringerung der Stolonenzuwachsrate mit steigender Temperatur (12°, 17°, 22° C). Die Reihenfolge der fördernden Wirkung der einzelnen Salzgehaltsstufen ergibt sich zu 32 , 24 , 16 , 40 S. Im Prinzip ähnliche Verhältnisse liegen hinsichtlich der asexuellen Vermehrungsrate vor. Bemessen an den getesteten Kriterien scheinen die Temperaturansprüche mit zunehmendem Koloniealter abzunehmen. Die errechneten doubling times sind wesentlich länger als beiCordylophora; möglicherweise deutet dieser Unterschied auf inadäquate Kulturbedingungen (Fütterung, Wasserbewegung) hin.

     

Eine mit Xenonbögen ausgerüstete Interferenzfilter-Monochromatoranlage für kurzwellige sichtbare und Langwellige ultraviolette Strahlung

Summary An interference filter monochromator system for biological purposes has been described. The system contains two monochromator units. It operates with xenon arcs (Osram XBO 501) as sources of radiation and is therefore especially adapted for experimental work in the blue-violet range of the visible spectrum and in the near ultraviolet (until about 350 m). All lenses are made of quartz. A circle of 8 cm diameter is homogenously irradiated. The irradiances which can be presently obtained within this circle with our single or double interference filters are rather high (1900 and 630 ergs/cm²·sec respectively at 355 m, 9000 and 1700 ergs/cm²·sec respectively around 450 m). Together with the monochromator system which we described recently (Mohr undSchoser 1959) and which operates with incandescent projection lamps this xenon arc system enables biological investigations with highly purified monochromatic radiation in the spectral range from 350 to 800 m.

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Microbial transformations in a cyclodextrin medium. Part 3. Cholesterol oxidation by Rhodococcus erythropolis

An intensive and systematic investigation of the oxidation of cholesterol (CL) to cholest-4-en-3-one (CN) by Rhodococcus erythropolis was undertaken in the presence of natural and chemically modified cyclodextrins (CDs) in a stirred bioreactor. The biotransformation was found to be strongly affected by the mode of addition of the natural CDs. While simultaneous addition of CL with either - or -CD led to a limited enhancement effect, the microbial oxidation of - and -CD complexes of CL was totally inhibited. In contrast, the alkylated CDs- dimethyl-, trimethyl- and hydroxypropyl--CD exhibited a remarkable enhancement of the microbial oxidation, irrespective of their mode of addition. The performance of the alkylated CDs was interpreted in the light of the measured phase solubility diagrams of CL and CN. It was thus shown that unlike the low solubilising power of hydroxypropyl--CD, dimethyl- and trimethyl--CD at 90 mm each, dissolved 9.3 and 8.7 g/l of CL and CN, respectively. Further investigation focused on the formation of CD complexes with CL and CN, analysed by X-ray powder diffractometry, differential scanning calorimetry and ¹H-nuclear magnetic resonance. It was thus shown that -CD forms a 2:1 CD:CL and CD:CN water-insoluble complexes. A mechanism of the biotransformation in homogeneous and heterogeneous CD media was presented while suggesting a direct interaction of the CD-substrate complex with microbial cells. Correspondence to: R. Bar     

Detergent sensitivity and splitting of isolated liver gap junctions

Summary Isolated rat liver gap junctions were split by two methods. In the first method, isolated gap junctions were stabilized by cross-linking their cytoplasmic surfaces with glutaraldehyde under conditions that prevented the entry of glutaraldehyde into the gap region. The stabilized junctions were then split in the junctional gap with SDS. In the second procedure, unfixed gap junctions were split by incubation in ureacontaining solutions. Junctional splitting was monitored by electron microscopy of thin sectioned and freeze fractured membrane pellets. Sidedness of the split junctional membranes was defined by labeling their cytoplasmic surfaces with glutaraldehyde-activated ferritin before splitting with urea. Gap junctional splitting did not result in any loss of protein components as determined by SDS-gel electrophoresis. The glutaraldehyde cross-linking procedure was also used to determine the effects of various detergents on the protein-protein interactions in the gap region. Of the detergents tested, only SDS caused junctional splitting.     

Determination of protein oligomeric structure from small‐angle X‐ray scattering

Small‐angle X‐ray scattering (SAXS) is useful for determining the oligomeric states and quaternary structures of proteins in solution. The average molecular mass in solution can be calculated directly from a single SAXS curve collected on an arbitrary scale from a sample of unknown protein concentration without the need for beamline calibration or protein standards. The quaternary structure in solution can be deduced by comparing the experimental SAXS curve to theoretical curves calculated from proposed models of the oligomer. This approach is especially robust when the crystal structure of the target protein is known, and the candidate oligomer models are derived from the crystal lattice. When SAXS data are obtained at multiple protein concentrations, this analysis can provide insight into dynamic self‐association equilibria. Herein, we summarize the computational methods that are used to determine protein molecular mass and quaternary structure from SAXS data. These methods are organized into a workflow and demonstrated with four case studies using experimental SAXS data from the published literature.     

Rapid detection of single nucleotide deletions: application to the β 6 (-A) mutation of the β-globin gene and to cystic fibrosis

The formation of heteroduplexes from the amplified products of homologous alleles has been shown to be useful in the identification of heterozygotes carrying deletion or insertion mutations. Here, we describe an improved procedure that allows the detection of single base pair (bp) deletions on nondenaturing polyacrylamide gels. Carriers for a common Mediterranean -thalassemic mutation, 6 (-A), could be easily detected by use of this method, as could carriers of a 1-bp deletion in the cystic fibrosis gene.     

Biospeciation, by potentiometry and computer simulation, of Sm-EDTMP, a bone tumor palliative agent

¹⁵³Sm-EDTMP (ethylenediaminetetra(methylenephosphonic) acid) is of considerable interest as a bone therapeutic radiopharmaceutical but its properties in solution are not yet well characterized. The protonation constants of EDTMP and the formation constants of the complexes of Sm-EDTMP have accordingly been measured potentiometrically by glass electrode titrations at 25°C in 0.15 M NaCl. Six protonation constants (log ₀₁₁ = 9.638, log ₀₁₂ = 17.330, log ₀₁₃ = 23.597, log ₀₁₄ = 28.636, log ₀₁₅ = 31.501, log ₀₁₆ = 32.624) and the formation constants of the [Sm(EDTMP)H_-1]^6- (log _11-1 = 4.865), [SmEDTMP]^5- (log ₁₁₀ = 12.018), [Sm(EDTMP)H]^4- (log ₁₁₁ = 17.892) and [Sm(EDTMP)H₂]^3- (log ₁₁₂ = 23.437) complexes were determined. Computer simulations indicate that the [SmEDTMP]^5- and the hydroxy [Sm(EDTMP)H_-1]^6- species are the major Sm(III) complexes formed in blood plasma, which explains the high degree of localization in the kidney and urine observed in biodistribution studies. Calcium ions are probably the maior competitor for EDTMP in blood plasma. As the presence of secondary skeletal metastases results in a high rate of bone turnover, it is possible that the high concentration of calcium at these sites encourages localization of ¹⁵³Sm-EDTMP.     

Nucleotide sequence of a promoter recognized by Bacillus subtilis RNA polymerase

Summary We report the nucleotide sequence of a promoter recognized by RNA polymerase from the gram-positive bacterium Bacillus subtilis. This promoter, which was isolated from B. subtilis phage SP01 DNA, is homologous to promoters for Escherichia coli RNA polymerase; the sequences of the -35 region and the Pribnow box were 5TTGACT and 5CATAAT, respectively (T is the thymine analog 5-hydroxymethyluracil in SP01 DNA). These sequences each differed by only a single base pair from the preferred sequences for E. coli promoters. Not surprisingly, the SP01 promoter was actively transcribed in vitro by E. coli RNA polymerase as well as by B. subtilis RNA polymerase.     

The biliary excretion of trypsin in rats

The serum half-life of bovine [³H]acetyltrypsin was estimated to be 9 rain following intravenous administration in rats. This was maintained when six successive doses of 200 g each were given at 1-h intervals. The enzyme was removed from the circulation after complexing with 2-macroglobulin (2-M). The amount of³H label appearing in bile increased with each successive dose and this was associated with breakdown products (<10 000 daltons) of the ₂–M/[³H] acetyltrypsin. Intact –M/[³H] acetyltrypsin was recovered from bile but represented only 0.06% of the administered dose of active enzyme.     

Fungal activities involved in lignocellulose degradation by Pleurotus

Summary During growth of Pleurotus on cotton straw both the straw in general and the lignin in particular were degraded. After 4 days of fungal growth, activity of laccase, catechol oxidase, peroxidase, and cellulase were detected. This activity, however, declined rapidly after 8–10 days of growth.Lignin degradation began after 10 days and reached a maximum after 21 days. It would seem that the preliminary action of laccase is a prerequisite for lignin degradation.The Pleurotus ostreatus strain P₃ had no detectable laccase activity and showed very poor ability to degrade cotton straw and lignin.Water extract of cotton straw was found to be a potent inducer of laccase in liquid medium and had an effect much stronger than several small phenolic compounds. The degradation of washed cotton straw and lignin from this straw was lower than native straw, so was laccase activity on this medium. High carbon dioxide concentrations encouraged straw degradation by P. ostreatus florida but severly limited lignin degradation. Other fungi including the known lignin degrader Phanarochaete chrysosporium were able to degrade up to 40% of cotton straw dry weight within 21 days of fungal growth. The percentage degradation of lignin, however, was very low (only 10% in 21 days). Pleurotus ostreatus florida was able to degrade up to 56% of the lignin within this time.After treatment with P. ostreatus florida almost four times as much glucose was released when the straw was treated with commercial cellulases, showing increased availability of cellulose.It is suggested that treatment with P. ostreatus florida may be used to enrich low value food materials for ruminant animals.     

Colour saturation triggers innate reactions to flower signals: Flower dummy experiments with bumblebees

Summary Innate behavioural reactions, i.e. reactions of untrained, flower-naive bumblebees (Bombus terrestris L., B. lucorum L.; Apidae) were observed in flower dummy experiments. It was proven that an innate releasing mechanism responds to optical flower signals: the spectral purity of corolla colour was found to be crucial for far attraction toward flower dummies. During the subsequent near orientation, that is when a bumblebee finally reaches a flower dummy, the bumblebee's antennae contact the part of highest spectral purity while the bee is still in flight. Guides such as stamen patches present in the center of flower dummies are used only for near orientation. Flower dummies receiving the greatest number of antennae reactions at the guide were always those with low spectral purity in the surrounding background colour, high spectral purity at the corolla colour and highest spectral purity at the guide colour. In contrast, dominant wavelength and intensity of flower dummy colours had no detectable influence on innate behavioural reactions, while colour contrast had some. These results are interpreted as follows: orientation toward guides is based upon a gradient of centripetally increasing, bee-subjective colour saturation which directs the bumblebee's approach toward the center of the flower dummy where additional factors may contribute to stimulating the landing reaction.     

The problem with zeroes: why don't drosophilids lay eggs?

Summary We present some data on drosophilid oviposition and analyse the distribution of egg numbers over patches using an iterated negative binomial. This suggests that there are three different reasons for empty patches; patches are not found, patches are not suitable, or females are not able to lay eggs. This leads to five categories of site which can be disentangled using the iterated negative binomial. Since empty patches have important consequences for population dynamics and coexistence, this analysis will highlight how microscopic processes influence macroscopic behaviour in population biology.