BOOK REVIEWS

Book reviewed in this article: Lieth, H. & Schwartz, M.D. (eds.) 1997. Phenology in seasonal climates I . Progress in Biometeorology, Vol. 12. 143 pp. Backhuys Publishers, Leiden. ISBN 90–73348–79-X. Price: USD 42.25.     

Reviews

Book reviewed in this article:
Maydell, H.-J. von. 1990. Trees and Shrubs of the Sa-hel: their characteristics and uses.
Braun, M., Burgstaller, H., Hamdoum, A. M. & Walter, H. 1991. Common Weeds of Central Sudan.     

Reviews of publications

Book reviewed in this article:
Stratification of a tropical forest as seen in dispersal types , by Ingrid Roth. Tasks for Vegetation Science, 17 (Eds H. Lieth & H. Mooney), Dordrecht, Boston & Lancaster: Dr W. Junk 1987
Genetic Aspects of Plant Mineral Nutrition , edited by W. H. Gabelman & P. C. Loughman.     

The thrombospondin motif of aggrecanase-1 (ADAMTS-4) is critical for aggrecan substrate recognition and cleavage

Aggrecanase-1 (ADAMTS-4) is a member of the a disintegrin and metalloprotease with thrombospondin motifs (ADAMTS) protein family that was recently identified. Aggrecanase-1 is one of two ADAMTS cartilage-degrading enzymes purified from interleukin-1-stimulated bovine nasal cartilage (Tortorella, M. D., Burn, T. C., Pratta, M. A. , Abbaszade, I., Hollis, J. M., Liu, R., Rosenfeld, S. A., Copeland, R. A., Decicco, C. P., Wynn, R., Rockwell, A., Yang, F., Duke, J. L., Solomon, K., George, H., Bruckner, R., Nagase, H., Itoh, Y., Ellis, D. M., Ross, H., Wiswall, B. H., Murphy, K., Hillman, M. C., Jr., Hollis, G. F., and Arner, E.C. (1999) Science 284, 1664-1666; 2 Abbaszade, I., Liu, R. Q., Yang, F., Rosenfeld, S. A., Ross, O. H., Link, J. R., Ellis, D. M., Tortorella, M. D., Pratta, M. A., Hollis, J. M., Wynn, R., Duke, J. L., George, H. J., Hillman, M. C., Jr., Murphy, K., Wiswall, B. H., Copeland, R. A., Decicco, C. P., Bruckner, R., Nagase, H., Itoh, Y., Newton, R. C., Magolda, R. L., Trzaskos, J. M., and Burn, T. C. (1999) J. Biol. Chem. 274, 23443-23450). The aggrecan products generated by this enzyme are found in cartilage cultures stimulated with cytokines and in synovial fluid from patients with arthritis, suggesting that aggrecanase-1 may be important in diseases involving cartilage destruction. Here we demonstrate that the thrombospondin type-1 (TSP-1) motif located within the C terminus of aggrecanase-1 binds to the glycosaminoglycans of aggrecan. Data from several studies indicate that this binding of aggrecanase-1 to aggrecan through the TSP-1 motif is necessary for enzymatic cleavage of aggrecan. 1) A truncated form of aggrecanase-1 lacking the TSP-1 motif was not effective in cleaving aggrecan. 2) Several peptides representing different regions of the TSP-1 motif effectively blocked aggrecanase-1 cleavage of aggrecan by preventing the enzyme from binding to the substrate. 3) Aggrecanase-1 was not effective in cleaving glycosaminoglycan-free aggrecan. Taken together, these data suggest that the TSP-1 motif of aggrecanase-1 is critical for substrate recognition and cleavage.     

Horizon annealing: a collection‐based approach to automated sequencing of the fossil record

Sheets, H.D., Mitchell, C.E., Izard, Z.T., Willis, J.M., Melchin, M.J. & Holmden, C. 2012: Horizon annealing: a collection‐based approach to automated sequencing of the fossil record. Lethaia, Vol. 45, pp. 532–547. A number of different approaches to quantitative biochronology have been proposed and used to construct high‐resolution time‐scales for a range of uses. We present a new approach, horizon annealing, which uses simulated annealing to optimize the sequencing of collection horizons. Temporal sequences of events produced by this method are compared with those produced by graphic correlation, CONOP and RASC for a series of previously studied exemplar data sets. Horizon annealing produces results similar to other methods, but it does have properties (the ordination of collections and the avoidance of some local minima) that make it useful for high‐resolution studies, particularly those based on capture‐mark‐recapture methods requiring detailed presence–absence data for individual collections and taxa. □ Chronostratigraphy, graphic correlation, graptolite, rate of evolution, CONOP9.     

A Mathematical Model for Simultaneous Spatio-Temporal Dynamics of Calcium and Inositol 1,4,5-Trisphosphate in Madin–Darby Canine Kidney Epithelial Cells

The landmark paper by Hirose et al. (Hirose, K., Kadowaki, S., Tanabe, M., Takeshima, H., Iino, M., Science 284:1527–1530, 1999) presented experimental investigations to show that not only can calcium upregulate IP₃, but that it can also have an inhibitory effect on IP₃. In this paper, we present a preliminary model, which is consistent with these experiments. This model includes positive and negative feedback between calcium and IP₃ and is able to reproduce more precisely the data presented in Hirose et al. (Hirose, K., Kadowaki, S., Tanabe, M., Takeshima, H., Iino, M., Science 284:1527–1530, 1999). In the second part of the paper, the intracellular and intercellular calcium movement in Madin–Darby canine kidney epithelial cells is investigated. With the aid of the model we are able to identify the aspects of IP₃ and calcium signalling, which should be studied further experimentally before refining the model.     

BOOK REVIEWS

Lambers, H., Poorter, H. & Van Vuuren, M. (eds.) 1998. Inherent variation in plant growth: Physiological mechanisms and ecological consequences. Schmidt‐Vogt, D. 1999. Swidden farming and fallow vegetation in northern Thailand.     

Other short reviews

Wiedemann, A.M., Dennis, L.R.J. & Smith, F.H. 1999. Plants of the Oregon coastal dunes. (New edition). 120 pp. Oregon State University Press, Corvallis, OR. ISBN 0–87071–457–0. (paperback) Price: USD 12.95.     

Alternating zinc fingers in the human male-associated protein ZFY: HX3H and HX4H motifs encode a local structural switch

The two-finger repeat in the human male-associated protein ZFY provides a model for comparative 2D-NMR studies of classical and variant Zn fingers. This repeat is defined in part by an alternation in spacing between consensus (HX3H) and variant (HX4H) histidine spacings. To investigate the effects of a "switch" between alternative histidine spacings, we have designed an HX3H analogue of a representative HX4H domain of known structure [ZFY-6; Kochoyan, M., Havel, T., Nguyen, D. T., Dahl, C. E., Keutmann, H. T., & Weiss, M. A. (1991) Biochemistry 30, 3371-3386]. The HX3H analogue (designated ZFY-switch) forms a tetrahedral Co2+ complex whose thermodynamic stability is similar to that of the parent peptide. 2D-NMR studies demonstrate that ZFY-switch and ZFY-6, although similar in overall structure, exhibit significant local changes near the site of deletion. Whereas the HX4H site in the native finger forms a nonstandard loop, the HX3H site in ZFY-switch folds as a 3(10) extension of the C-terminal alpha-helix, as observed in the NMR solution structure of a consensus HX3H domain [Lee, M. S., Gippert, G. P., Soman, K. V., Case, D. A., & Wright, P. E. (1989) Science 245, 635-637] and in the crystal structure of a representative Zn finger-DNA complex [Pavletich, N. P., & Pabo, C. O. (1991) Science 252, 809-817]. We propose that variant histidine spacings (HX3H and HX4H) encode a local switch between alternative surface architectures with implications for models of protein-DNA recognition.     

Recent advances in the molecular analysis of inherited disease

Many important human genes have been cloned during the last ten years. In some cases, using reverse genetic techniques [Orkin, S. H. (1986) Cell 47, 845-850], disease-causing genes have been isolated whose product was previously unknown. Important examples include the dystrophin protein which, when mutated, gives rise to either Duchenne or Becker muscular dystrophy [Koenig, M., Hoffman, E. P., Bertelson, C. J., Monaco, A. P., Feener, C. and Kunkel, L. M. (1987) Cell 50, 509-517; Monaco, A. P., Bertelson, C. J., Liechti-Gallati, S. & Kunkel, L. M. (1988) Genomics 2, 90-95; Koenig, M., Monaco, A. P. & Kunkel, L. M. (1988) Cell 53, 219-228] and the cystic fibrosis transmembrane conductance regulator (CFTR) [Riordan, J. R., Rommens, J. M., Kerem, B.-S., Alon, N., Rozmahel, R., Grzelczak, Z., Zielenski, J., Lok, S., Plavsic, N., Chou, J.-L., Drumm, M. L., Ianuzzi, M. C., Collins, F. S. & Tsui, L.-C. (1989) Science 245, 1066-1073]. Recently the technology for systematically detecting single base-pair changes by chemical methods, enzymatic methods or direct DNA sequencing has greatly expanded and simplified. In addition to providing structural information about these clinically important genes and information on disease-causing mutations, these studies have led to an increased understanding of mechanisms of mutation, to the discovery of novel genetic mechanisms and to important clinical applications of carrier detection and pre-natal diagnosis. The recent rapid progress has been made possible by the development of DNA amplification using the polymerase chain reaction (pcr) invented by Saiki and colleagues [Saiki, R. K., Chang, C-A., Levenson, C. H., Warren, T. C., Boehm, C. D., Kazazian, H. H. & Ehrlich, H. A. (1988) N. Engl. J. Med. 319, 537-541].     

Rhabditophanes schneideri (Rhabditida) phoretic on a cave pseudoscorpion

Information of phoretic nematode-pseudoscorpion associations and cases of parasitism on five European species of pseudoscorpions was summarized by Cur?ic et al. [Curci?, B.P.M., Dimitrijevi?, R.N., Makarov, S.E., Luci?, L.R., Curci?, S.B., 1996. Further report on nematode-pseudoscorpion associations. Acta arachnol. 45, 43-46; Curci?, B.P.M., Sudhaus, W., Dimitrijevi?, R.N., Tomi?, V.T., Curci?, S.B., 2004. Phoresy of Rhabditophanes schneideri (Bütschli) (Rhabditida: Alloionematidae) on pseudoscorpions (Arachnida: Pseudoscorpiones). Nematology 6 (3), 313-317]. An examination of a sample of the cavernicolous pseudoscorpion Neobisium rajkodimitrijevici (Curci? and Tomi?, 2006) (comprising a holotype male and a paratype tritonymph) from a cave in Eastern Serbia revealed this false scorpion to be a nematode carrier; the present paper reports this finding and extends our knowledge of phoresy of Rhabditophanes on pseudoscorpions. This is the first time that the rhabditid R. schneideri (Bütschli, 1873) has been noted in association with a cavernicolous pseudoscorpion. There must be some patchily distributed micro-habitats in caves where saprobiotic nematodes and small arthropods can complete their life-cycles, for example something like deposits of bat guano. The transportation of Rhabditophanes J3 by pseudoscorpions indicate that Neobisium specimens often visit these micro-habitats to find their prey.     

Secretion and assembly of type IV and VI collagens depend on glycosylation of hydroxylysines

Most lysines in type IV and VI collagens are hydroxylated and glycosylated, but the functions of these unique galactosylhydroxylysyl and glucosylgalactosylhydroxylysyl residues are poorly understood. The formation of glycosylated hydroxylysines is catalyzed by multifunctional lysyl hydroxylase 3 (LH3) in vivo, and we have used LH3-manipulated mice and cells as models to study the function of these carbohydrates. These hydroxylysine-linked carbohydrates were shown recently to be indispensable for the formation of basement membranes (Ruotsalainen, H., Sipil?, L., Vapola, M., Sormunen, R., Salo, A. M., Uitto, L., Mercer, D. K., Robins, S. P., Risteli, M., Aszodi, A., F?ssler, R., and Myllyl?, R. (2006) J. Cell Sci. 119, 625-635). Analysis of LH3 knock-out embryos and cells in this work indicated that loss of glycosylated hydroxylysines prevents the intracellular tetramerization of type VI collagen and leads to impaired secretion of type IV and VI collagens. Mice lacking the LH activity of LH3 produced slightly underglycosylated type IV and VI collagens with abnormal distribution. The altered distribution and aggregation of type VI collagen led to similar ultrastructural alterations in muscle to those detected in collagen VI knockout and some Ullrich congenital muscular dystrophy patients. Our results provide new information about the function of hydroxylysine-linked carbohydrates of collagens, indicating that they play an important role in the secretion, assembly, and distribution of highly glycosylated collagen types.     

Methods for aligning and for averaging 3D volumes with missing data

The visibility and resolution of a tomographic reconstruction containing multiple copies of discrete particles can be enhanced by averaging subtomograms after they are corrected aligned. However, the “missing wedge” in electron tomography can easily lead to erroneous alignment. We have explored a Fourier space cross-correlation method with a proper weighting scheme to align and average different sets of volumetric data, each of which has different missing data due to the limited specimen tilts. This approach depends neither on a preexisting template, nor an exact knowledge of the geometry, orientation, or amount of the missing data. This paper introduces a procedure where the missing data might be gradually “filled in” by consecutively aligning and averaging volumes with different orientations of their missing data. We have validated these techniques by a set of simulated data with various symmetries and extent of missing data. We have also successfully applied these procedures to experimental cryo-electron tomographic data [Chang, J.T., Schmid, M.F., Rixon, F.J., and Chiu, W., 2007. Electron cryotomography reveals the portal in the herpesvirus capsid. J. Virol. 81, 2065–2068; Schmid, M.F., Paredes, A.M., Khant, H.A., Soyer, F., Aldrich, H.C., Chiu, W., and Shively, J.M., 2006. Structure of Halothiobacillus neapolitanus carboxysomes by cryo-electron tomography. J. Mol. Biol. 364, 526–535].     

Fluorescence energy transfer measurements of spatial relationships between sulfhydryl groups of thiolase I from porcine heart

Mitochondrial thiolase I from pig heart has been found to have at least two and possibly three reactive sulfhydryl residues at or near the active site [Izbicka-Dimitrijevi?, E., & Gilbert, H. F. (1982) Biochemistry 21, 6112-6118; Izbicka-Dimitrijevi?, E., & Gilbert, H. F. (1984) Biochemistry 23, 4318-4324]. In the native enzyme, fluorescein mercuric acetate reacts with two of the sulfhydryl groups and inactivates the enzyme with a rate constant of 1.6 X 10(-4) M-1 s-1 in 0.1 M Tris-acetate, pH 7.0. The presence of saturating (250 microM) concentrations of acetoacetyl coenzyme A protects against both modification and inactivation. The acetyl enzyme, a normal intermediate in the reaction catalyzed by thiolase, is not inactivated by fluorescein mercuric acetate although one sulfhydryl group out of five per mole of thiolase subunit is still available for reaction with the reagent. Fluorescein mercuric acetate and S-mercurio-N-dansyl-L-cysteine (Dns-Cys-SHg+) have been used to differentially label two of the sulfhydryl groups in thiolase. The distance between Dns-Cys-SHg+ (donor) and fluorescein mercuric acetate (acceptor) determined by the fluorescence energy transfer is less than 14 A. The fluorescent analogue of coenzyme A, 1,N6-etheno coenzyme A, is recognized by thiolase as a substrate (Km = 21 microM); however, substrate inhibition and equilibrium dialysis show that the affinity of the free enzyme for CoA is quite low (Ki = 100 microM). The quantum yield of the fluorescence of the three thiolase tryptophan residues is low (0.024), corresponding to about 12% of the fluorescence expected from equivalent concentrations of tryptophan.     

Novel Structural and Functional Insights into M3 Muscarinic Receptor Dimer/Oligomer Formation

Class A G protein-coupled receptors (GPCRs) are able to form homodimers and/or oligomeric arrays. We recently proposed, based on bioluminescence resonance energy transfer studies with the M₃ muscarinic receptor (M3R), a prototypic class A GPCR, that the M3R is able to form multiple, structurally distinct dimers that are probably transient in nature (McMillin, S. M., Heusel, M., Liu, T., Costanzi, S., and Wess, J. (2011) J. Biol. Chem. 286, 28584–28598). To provide more direct experimental support for this concept, we employed a disulfide cross-linking strategy to trap various M3R dimeric species present in a native lipid environment (transfected COS-7 cells). Disulfide cross-linking studies were carried out with many mutant M3Rs containing single cysteine (Cys) substitutions within two distinct cytoplasmic M3R regions, the C-terminal portion of the second intracellular loop (i2) and helix H8 (H8). The pattern of cross-links that we obtained, in combination with molecular modeling studies, was consistent with the existence of two structurally distinct M3R dimer interfaces, one involving i2/i2 contacts (TM4-TM5-i2 interface) and the other one characterized by H8-H8 interactions (TM1-TM2-H8 interface). Specific H8-H8 disulfide cross-links led to significant impairments in M3R-mediated G protein activation, suggesting that changes in the structural orientation or mobility of H8 are critical for efficient receptor-G protein coupling. Our findings provide novel structural and functional insights into the mechanisms involved in M3R dimerization (oligomerization). Because the M3R shows a high degree of sequence similarity with many other class A GPCRs, our findings should be of considerable general interest.     

Schistosoma mansoni:The Circulating Cathodic Antigen Forms an Abundant Product of 41/42 kDa in the Urine of Infected Patients

Abdeen, H. H., Attallah, A.-F. M., El-Mohamady, H. I., Harrison, R. A., and Mansour, M. M. 1998.Schistosoma mansoni: The circulating cathodic antigen forms an abundant product of 41/42 kDa in the urine of infected patients.Experimental Parasitology90, 286–289.     

Dormancy and germination responses of halophyte seeds to the application of ethylene

Ethylene is invariably produced during seed germination but its role in regulating seed dormancy and germination is poorly understood. Seeds of 22 halophytic species having different life forms – salt secreting dicots, salt secreting monocots, stem succulents and leaf succulents were germinated in Petri dishes kept in a growth chamber set at 20/30 °C (night/day) temperature and a 12 hr light period. Sodium chloride and ethephon were added to the medium from the beginning of the experiment. Seed germination was recorded every other day for twenty days. Application of ethylene did not have any significant effect on releasing seeds from innate dormancy. However, it appeared to have a role in alleviation of salinity effects which varied from negative in certain species to almost complete alleviation of high salinity effects in others.Our data indicates that ethylene appears to have little role in breaking innate seed dormancy however, in most halophyte seeds studied, application of ethylene alleviate the salinity effect to various degrees. Halophyte seeds which could germinate under saline conditions approaching twice the salinity of seawater may offer clues to understand management of seed germination under highly saline conditions. To cite this article: M.A. Khan et al., C. R. Biologies 332 (2009).     

Isolation and structural characterization of an insulin-related molecule, a predominant neuropeptide from Locusta migratoria

Neurohaemal lobes of corpora cardiaca of Locusta migratoria are an established storage site for neurohormones produced by the neurosecretory cells of the brain. As previously reported [Hietter, H., Van Dorsselaer, A., Green, B., Denoroy, L., Hoffmann, J.A. & Luu, B. (1990) Eur. J. Biochem. 187, 241-247], the isolation and characterization of a novel 5-kDa peptide from these lobes served as the basis for oligonucleotide screening of cDNA libraries prepared from poly(A) RNA from neurosecretory cells of the central nervous system. From subsequent cDNA cloning studies [Lagueux, M., Lwoff, L., Meister, M., Goltzené, F. & Hoffmann, J.A. (1990) Eur. J. Biochem. 187, 249-254], the existence of a 145-residue precursor protein was deduced, which contained, in addition to the 5-kDa peptide, amino-acid sequences with homology to the A and B chains of an insulin-related peptide. In the present study we have isolated the native molecule from corpora cardiaca of Locusta and characterized, by Edman degradation and plasma-desorption mass spectrometry, the two chains as follows: A chain, Gly-Val-Phe-Asp-Glu-Cys-Cys-Arg-Lys-Ser-Cys-Ser-Ile-Ser-Glu-Leu-Gln-Thr- Tyr-Cys - Gly (Ile, isoleucine); B chain, Ser-Gly-Ala-Pro-Gln-Pro-Val-Ala-Arg-Tyr-Cys-Gly-Glu-Lys-Leu-Ser-Asn-Ala- Leu-Lys - Leu-Val-Cys-Arg-Gly-Asn-Tyr-Asn-Thr-Met-Phe. Taken in conjunction with the previous cloning studies, our data lead to a clear picture of the processing of Locusta preproinsulin. They indicate that locusta corpora cardiaca contain remarkably large amounts of one single insulin form, in contrast to multiple insulin isoforms of Bombyx mori, the only other insect species from which insulin-related peptides have been isolated and characterized [Nagasawa, H., Kataoka, H., Isogai, A., Tamura, S., Suzuki, A., Mizoguchi, A., Fujiwara, Y., Suzuki, A., Takahashi, S. & Ishizaki, H. (1986) Proc. Natl Acad. Sci. USA 83, 5840-5843].     

Proton release upon oxidation of tyrosine in reaction centers from Rhodobacter sphaeroides

Markedly different light-induced protonational changes were measured in two reaction center mutants of Rhodobacter sphaeroides. A quadruple mutant containing alterations, at residues L131, M160, M197, and M210, that elevate the midpoint potential of the bacteriochlorophyll dimer was compared to the Y(M) mutant, which contains these alterations plus a tyrosine at M164 serving as a secondary electron donor [Kálmán et al., Nature 402 (1999) 696]. In the quadruple mutant, a proton uptake of 0.1-0.3 H(+)/reaction center between pH 6 and 10 resulted from formation of the oxidized bacteriochlorophyll donor and reduced primary quinone. In the Y(M) mutant, a maximal proton release of -0.5 H(+)/reaction center at pH 8 was attributed to formation of the tyrosyl radical and modeled using electrostatic and direct proton-releasing mechanisms.